10.6.4 Woes - Read many threads but still need help!

Howdy all!
Here's the deal, I'm having problems which I can only trace back to the upgrade to 10.6.4. Everything seemed to be fine for a couple of weeks but something happened when I set-up my new office in my house (external monitor, hard drives etc) I've read so many threads and have tried different things but now am at a loss. I'm way out of warranty so I can even go to the Genius bar or will they charge me? Here's the gist.
Symptoms:
A) Long boot on gray screen, once finder is open the system is frozen for like 10 minutes, dock won't pop up etc. Mouse can move but won't click anything. After 10 minutes things seem to be fine.
B) Computer won't wake up from sleep mode (like if I close the laptop cover) but it will wake-up if the display has gone off
C) Firewire seems to no longer work
Here's what I have tried already:
1) Installed the combo update (fresh download)
2) Repaired permissions (several times and it keeps finding them)
3) Trashed my firewire port (no change)
4) Disable airport (and basically what happens when I do this is that instead of waiting 10 minutes with just a mouse arrow, I have a beachball (non-spinning) for 10 minutes which then disappears when the machine decides to work) At one point I had a hazy blue screen over my desktop and that disappeared after 10 minutes but I've only had that happen one time
5) My disk is OK per Disk Utility, and it says its S.M.A.R.T. status is enabled (or whatever it is supposed to say I forget at the moment but I checked it as one thread suggested and it was as it is supposed to be)
6) The machine boots fine in safe mode - though it is still a long boot but you can use it as soon as the finder loads.
7) The only thing I haven't done is zap my pram (will this help?) and how do you do it?
Thoughts? I can roll back to 10.6.3 which I know has pros and cons but at least it works.
My Applecare ran out and I'm pretty broke at the moment so I don't want to pay for support if I don't have to (although it's more than I don't want to spend a lot of time at the Apple Store to find out something I already know - that 10.6.4 is buggy!(
Help please and thanks so much! Sorry for the long post but I thought I would try to save some questions. I've read so many threads it was all running together.

Oh and yet a new symptom - I can't seem to sync my iPhone 3G. I could sync the photos to iPhoto, but not iTunes, it keeps timing out!

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