Slow boot up of 2008 macbook pro - Firewire port problem?

My 2008 15" macbook pro mostly works fine, but whenever I shut it down or restart it (as opposed to just sending it to sleep) it gets stuck trying to reboot. It usually takes several attempts, and so far, eventually starts if I leave it for a while, like a few hours.
I try all the basic things, resetting Pvram, trying safety mode, checking the disk for errors in disk utility, but they don't help at all.
It's been like this for about 6 months now, I mostly just never shut it down as it wakes up from sleep mode fine. But I'd like to find out what the problem is as every time I need to restart it I panic that it will never come back on again. Recently I booted it in verbose mode to see what the problem is and I'm getting a never ending error message saying something like this:
FIrewire (OHCI) TI ID 8025 built-in: handleUnrecoverableErrorInt
Seems like it's a problem wth my Firewire Port? I have never used Firewire, so wondered if I could just disable it somehow? my problem seems similar to this guy:
https://discussions.apple.com/message/9001641?searchText=Long%20boot%20up%20time s%202008%2015%22%20Macbook%20pro%20-%20firewire%20port%20problem?
But I'm a bit clueless so I'm not sure if his problem is the same... mine seems to be mostly related to boot up rather than kernal panic (I have no idea what that is to be honest!) and I don't want to just try his fix and break my computer!
My cd/dvd drive also stopped working around the same time, coincidentally the above post also says his drive is not working, I'm not sure if the two issues could be related?
Any thoughts advice much appreciated!
P.S. The machine has already had a new motherboard and graphics card put in by Apple as per the recall on this model

Ok, I copied the guy in the above thread and disabled my firewire by deleting this file:
/System/Library/Extensions/IOFireWireFamily.kext
Tested it a couple of times and it seems to have solved my slow boot up problem! I'm down from a 3 hour boot up to a minute or so!
Now, bizarrely, it won't shut down properly... I get stuck at a grey screen when I try to shut down, so I just have to press the dreaded power button. No idea why, but still, I'd rather it powered up properly, so I guess I'll just leave it as it is, I rarely shut it down fully anyway.

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