System unstable, not sure why?

[asktoby]

I've had XBMC running on my softmodded Xbox with a 80GB hard disk for quite a few years but never really used it much.
Recently I decided to get it out of retirement and update it.
The update went well. I installed the latest 3.5 XBMC and also Visionary 4.
With use, however, I found that it was crashing in certain games after around 15 minutes. It would happen in specific games, like Rallisport Challenge (disc) or TMNT The Arcade Game (ROM), but not in others like Rampage (ROM) or Panzer Dragoon Orta (disc).
Thermal?
I initially thought it might be overheating, maybe due to perished thermal paste. I removed the CPU and GPU heatsinks, cleaned them, and reapplied thermal paste.
This didn't help.
I also noticed that the system wasn't getting too hot either. After a crash I booted straight back into XBMC to check the temperatures and they were typically CPU:60°, GPU 44-50°.
I've also left XBMC on the temperature monitoring page today and found it to crash at just CPU:41°, GPU 46°.
Hard disk?
This led me to think that the HD might be at fault.
I reverted to my stock HD and cloned it to a different 80GB drive that I had available, for a fresh start.
Things seemed to be going well, until I tried to FTP Visionary 4 to F:, but now I'm finding that it's freezing after 15 minutes of just sitting on the XBMC desktop.
Other hardware issues?
I've inspected the mobo, can't see any damage, none of the capacitors are swollen.
Weird restore behaviour
After a freeze, I can't boot it again, getting the "3 boot attempts and then FRAG" (Flashing green and red, "Christmas lights").
I've found that if I leave it unplugged for around 12 hours I can get it to boot by holding both thumbsticks and getting into EvoX, launching XBMC from there. Quite what happens in those 12 hours I do not know. It can't be heat, because the system is cold after 30 minutes but it takes longer than that to recover.
Perhaps some kind of capacitance discharge? I've tried disconnecting the Xbox from the mains and then shorting the power supply pins for 15 seconds, that doesn't speed up the FRAG recovery.
I'm honestly baffled as to what could be wrong and am looking for suggestions.
Hardware modifications: SPDIF output mod, new heatsinks, new hard disk.

[xboxprince]

im not an expert so ill do my best to tell whats up. since you said your getting christmas lights you may have a bad tsop and i beleive installing a modchip should do the trick to fix that. when you get the christmas lights is it a blank screen or is there a specific error code that comes up?

EDIT: also check your clock cap

[asktoby]

I'm also no expert, thanks for chiming in!

When the boot fails it goes to a blank black screen.

TSOP
From my reading, the TSOP or EEPROM on a soft-modded Xbox is read-only, so it seems unlikely that it's been corrupted?
Anyway, it looks easy enough to do, even without a modchip:
1) Solder two points as per http://www.biline.ca/xbox_mod.htm
2) Flash BIOS via EvoX UI to Xecuter 4981 as it's 256KB and fits on all motherboard versions up to 1.5.

Clock cap
Open the box, inspect the clock cap for bulging or discharge.
Identify if I'm an Xbox 1.0 or 1.1.
Since I'm softmodded, use HeXEn before removal to make sure my softmod is up to date, and upgrade UnleashX, to avoid clock loops
If I am 1.0 or 1.1, completely remove the clock cap.

I'm out of ideas so I'll try those!

[xman]

Seeing as you are running a softmod, how about you show us your C drive using XBMC's filemanager and the take a screen shot of it?. That way the soft mod guys can potentially see any issues with the softmod. An alternative would be to show the XBMC log file and that way, if the problem is a software problem it can be identified in the log. If it is hardware related, short of having known good parts to exchange till the problem goes, the process is much harder. Your approach to checking the HDD is not sound. Have you considered what you cloned from one HDD to the other was in fact corrupted because the 1st HDD was damaged?. I would be inclined to do a fresh softmod install on the new HDD. Once that is working, if it does, then start adding your other content one at a time, checking each piece of new content at a time.