IPhone 3GS Charging/Battery Problem: Hardware, Software, or Both?

Question

Hello everyone,
I'm a long time Apple user, but this is the first time I've ever posted on the Apple Support forums. I hope you will please excuse the length of my post, as I believe that relaying the approximate sequence of events here is important in determining the cause (or causes) of the problem I am currently facing.
I've trawled the entire internet and I cannot find any reports of a problem that is actually identical to my own. There are many, many similar problems, but none of the exact nature or complexity that I am experiencing. I sincerely hope that someone who really knows their stuff will take the time to read through my story and offer some guidance, as this is my first iPhone and I want to be able to keep it!
I purchased the iPhone 3GS second-hand on eBay approx 3 weeks ago, to replace my old Nokia (which had finally given up the ghost), and although I initially got the 'charging is not supported with this accessory'  error - I remedied this problem by using a whole range of different chargers and USB cables which I had accumulated over the years, and so initially, I always managed to get the battery charged one way or the other.
For the record - the iPhone was in very good condition, but had been factory-reset by the seller, and so I upgraded to the latest compatible software (IOS 6.1.3) when I received it.
Anyhow, these charging methods included three different USB cables (OEM Apple ones), two different 3rd party (non-OEM) wall-chargers of differring design, and three different OEM Apple USB Power adaptors. You know - the Wall Socket with the USB slot in it.
There seeemed to be no discernibe pattern as to which charging device or combination of cables and sockets was the 'correct' or 'best' one to use, as the results were random. One charger would work one day, whilst another would work the next, and vice versa. I continued to swap chargers, plugs, and cables in order to get the thing charging. Despite any errors or problems, I would always manage to get it charged somehow, at least for the first week or two.
The only pattern I did discern was that the oldest of my USB cables, from a 2005 iPod Mini, did appear to be somewhat more reliable than the other, more modern cables - though at the same time, the newer cables did work (and charge the phone) on various occasions.
As things progressed though; the 'charging is not supported with this accessory'  error appeared on a more regular basis, though I was often able to get around it by changing plugs and/or leaving the device overnight. As many of you will undoubtedly know; this error message was said to be a 'software bug' - one which would typically appear once the battery's charge level was under 20%, and not before. Common advice on Mac forums was to never allow your battery level to drop below 20%, which would prevent the problem from occuring. 
However in my case, this error message was now showing up more regularly, often when the phone had more than 20% charge left, leaving me unable to charge the phone quickly and successfully when needed. 
And as many of you will also know, the 'official word' across all the different Mac forums is that even when this charging error message is showing, and the phone's battery indicator appears empty or declining, the battery will continue to charge, albeit at a much, much slower rate. This appeared to be true, as I was able to leave it overnight, with the error message displaying, and return to find that the battery had charged - though only to a marginal degree and never to full capacity. At this point, I was still able to use the phone, although on a somewhat limited basis, as the battery was always running out of juice too quickly.
However the situation worsened, whereby the phone started to reject all of the chargers and cables; either failing to recognize them at all, or giving me the aforementioned error message. Its battery would die,  and I would have to leave it plugged in overnight (approx 8-10 hours) to get any response out of it at all. If I left it long enough, it seemed that I would at least get some charge out of it, though the maximum charge level was rapidly decreasing despite the amount of time it had been charging for, making the phone become less and less usable by the day.
Still, things continued to worsen - the 'charging is not supported with this accessory'  error now appeared regardless of how much charge the battery had left in it, or what type of cables or plugs I was using - leaving me with no choice but to let the battery run down, and watch as the phone switched itself off..
Things have now reached the point where the phone is essentially unusable.
Strangely enough though; when completely dead or switched off, it will recognize the Apple USB to Wall Socket Charger, and will indicate that it IS charging - with the thin red line representing low battery levels, and a 'lightning bolt' logo underneath to signify the transfer of electrcity to the battery. Suffice to say, under these circumstances, the phone will charge, albeit very, very slowly, and only to a certain level (5-10%)
However - as soon as the phone is switched on again (either manually, or automatically - once it has reached a certain charge level) - the 'charging is not supported with this accessory' error appears immediately, and the phone immediately starts to lose power again, switching itself off again within a matter of minutes.
And so the cycle starts again - the phone is dead, it will accept the charger and indicate that it is charging (very slowly) until it comes back on again, at which point it rejects the charger (via the error message), runs out of power, and dies again. For every 4-5 minutes of use I get out of this phone before it dies again - I am having to charge it for hours and hours at a time; during which time the battery indicator never increases or gets beyond the red and into the green.
To confirm: when switched off - it appears to recognise the charger and will charge very, very slowly, but once switched on again - it rejects the charger and dies almost immediately due to lack of accumulated charge, regardless of charging time. The reason I explained the entire sequence of events here is that this did not just happen overnight, but rather progressively, with lots of random occurances and apparent technical contradictions along the way.
Another factor to consider is that I recently tried to charge it using the Apple USB Power Adaptors of two friends (both whilst the device was completely dead), to test whether my chargers and cables were somehow all at fault. The charger/adaptor for a new iPhone 4S did not work - but the charger for an older iPod Touch worked flawlessly, and gave me an immediate and efficient charge which lasted longer than any other, despite the limited amount of time I was able to leave it charging.
Having said that, due to the random behavior of this phone, I am uncertain whether this was simply a random occurance, or something technical relating to the charging equipment I was testing at the time.
It should also be noted that throughout this entire process - the phone will always register with iTunes when plugged into my laptop and switched on. I have had absolutely no trouble with the transferring or music or apps, or the updating of software since I got the device. Even today, where I managed to get a few minutes of 'on-time' out of the phone - it immediately registered with iTunes, despite simultaneously giving me the charging is not supported with this accessory' error, before promptly running out of power and dying again.
It will occasionally charge when connected to iTunes, but only at random and for extremely short periods of time.
If it's of any consequence, I am using a 2nd/3rd generation Macbook Pro from 2007, with a 2.16GHz Intel Core 2 Duo processor and 2GB of RAM, running OS X 10.5.8 (Snow Leopard). Snow Leopard has only recently been installed, and when installing it  - I did opt for a partial 'Time Machine' restore from a backup drive, which included key files and applications - but which did not restore my complete profile from the previous 'Leopard' OS.
Suffice to say - I am pulling my hair out here. You simply can't get by in today's world without a mobile phone, and I had only just bought this phone as a replacement for my old one. I had really come to depend on it, and would hate to think that I'd have to say goodbye to it because it required some kind of replacement part or repair that cost more than the phone itself (£65)
The only real, discernible pattern with these problems is that they continue to get worse. I've tried booking an appointment at my local 'Genius Bar' but their booking system has been down for a while, presumably due to high demand, and I also know that their policy is to try and sell you a replacement product or accessory before recommending or exploring any alternative solutions. Their policy is that they will not see you without an appointment anyway.
I have a feeling that although this may be hardware related on some level, with a potentially delicate or damaged charging port on the device itself - I've also read in many places that this is a software bug - which some of my experiences and observations would appear to confirm - especially as the phone can withstand lengthy and intensive procedures like the iTunes restore process (both in and out of recovery mode) without running out of power and dying. It seems to be getting fed enough power during these procedures, but not in any other situation - and will randomly charge in some circumstances, while not in others.
Thus far, I have tried:
- The 'Battery Doctor' App - which recognizes when the phone is charging, but doesn't alter the fact that it never seems to charge beyond about 5-10%, and has done nothing to change the fact that whilst apparently 'charging', the phone is still losing power and proceeds to die.
- A
- Cleaning the cables, adaptors and charging port with a toothbrush and some compressed air.
And still - the phone will appear to be charging when switched off (though it never seems to get beyond about 10%) and will stop charging as soon as it's switched on, leaving me with about 5 minutes of usage before I have to go through the whole process again.
Any advice whatsoever would be greatly appreciated - and again, my apologies for such a lengthy post!!
Thanking you in advance,
Adam

Answer 1

I have had your exact problem with my old 3GS, now I cannot even get it to turn on, I still see that it is supposed to be charging though, but it never charges any so it seems.
I replaced the Lower Dock Connector Assembly back when it still charged while hooked to my PC, and it found it made no real difference.
http://www.amazon.com/gp/product/B003Y5YXLK/ref=oh_details_o05_s00_i00?ie=UTF8&p sc=1 
At this point I am not sure if I should replace the battery and hope for the best, or just junk the phone, I cannot really sell it if I cannot reset it...