I like your work and returning to this thread to see your improvements each time! Thanks for sharing!
Some ideas that I never got round to on my slimline for your consideration:
For your situation of the fan clashing with the side of the case (I know you have changed fan (twice since then and...
Great stuff and great cable management! Thanks for sharing.
If you do put the cover back on, consider an extension to the fan shroud (so it is flush with the side of the case) to ensure it pulls fresh air from outside. Similar for the GPU. (I know it may be intolerable heat with the side on...
Good work with the CPU. Think the MB can do a lot more that the HP spec site says (although why would they...) eg. HP Irvine Motherboard: A List of CPU That Fit HP Irvine
Haven't tried more RAM. Can't say 8GB of DDR2 is economically easily achievable in my geography sadly :(
Consider BIOS...
I replaced the front facing USB ports with USB3 ones to utilise the upgraded MB header on this s3xxx case.
This was 50cm off length dual cable off eBay and loops round the edge of the case similar to the original cable. More work to do finishing the housing to make them stable...
Bought another Slimline off eBay. Standard inexplicable* no graphics problem.
Couldn't fix. Got a bit annoyed. Oven baked motherboard(!). It works again. Will probably fail again in time, to prolong will fix up a active cooling for the northbridge heatsink, let's see! :)
Probably a bit over-the-top / obstructed HDD cooling solution. But I might as well put a spare 80mm fan to use. ;)
Secured between edge of case, SATA cable pushing out and ziptie securing to ODD cage.
Have you looked in the Slimline case? If you are planning to stay in it please note you will struggle to fit the additional* SSD in (or at least it needs some thought). :)
Consider a Hybrid drive?
*additional to 3.5" HDD and ODD
Can you reach BIOS (first)?
I would try to isolate the fault as usual to a particular compnent by adding removing with ones you know are working. Also memtest to check RAM if you haven't already?
This is better than the 7750 right?
For those in the UK:
2GB version at £110 ($185)
http://www.overclockers.co.uk/showproduct.php?prodid=GX-058-KF (will need LP bracket separately (annoyingly))
That board will be too big for the s3000 variant cases.
You may have more luck(room) in a s5000 variant case.
Related but also separately here are some disassembly instructions for the s5000 case