IMac G5 project, now red light, overheating

So, I have this iMac G5 which has been quite problematic. It had couple bad capacitors so first I replaced few. Then it had artifacts, replaced even more, then it threw kernel panics, ended up replacing all caps. Now there are no artifacts or kernel panics, but the machin still hangs after operating some time. After that it has problems booting up, fans sometimes revving up and then doing while booting. I just now remembered that there was fourth led which would indicate overheating and yes, this led is lit when it does that weird fan revving. It does it usually only if the machine has first been on for a while, then crashed and after that when I try to power it up again. Apparently something is overheating and the machine cuts power off to prevent damage. I have tried to reset PRAM, SMU and also did those three codes in open firmware so all basic voodoo is done.
I find it strange that it does overheat even when I tried with the back cover off. Could it be a sad case that integrated heat sensor somewhere on the motherboard is damaged? As far as I know there are three sensors available, one for the processor, one external for the hard disk (gonna try unplugging that) and one inside the hard disk itself. Atleast there is three values that Temperature Monitor can detect.
Does anyone know if that red light appears only if the processor overheats or are there other sensors which affect? Any tips in general?

Well update to this. It seems now that the problem really is overheating. I tried to create shim between the GPU and the heatsink, I don't have copper plate (yet) so it is far from being optimal, I used couple layers of thermal conductive mat. After this the machine seemed to become stable atleast for that one time, I used it half an hour and it crashed only after I installed version update of OS X and tried to reboot. On next boot attempt there was again red led and fans max. but after a brief moment it booted. I noticed that even when I am running the machine with the back cover off and not doing anything disk intensive, the hard disk temperature is at 50 C which seems very high.
Then I decided to bring in normal fan (that you use to cool yourself) and adjust it blow directly to hard disk and at the GPU same time. After doing this (and of course the "shim" still in place) it seems that the machine is rock solid, played 3D games, surfed internet, ran Xbench and Rember and rebooted 3-4 times without the red led. Today I tried again with the fan on like before and the machine works just fine. Maybe the thermal material between the GPU and heatsink needs to be replaced or proper kind of shim applied. This thermal pad is still quite thick so if it has dried or something it might be that there has not really been connection with the heatsink at all and/or the real problem is the temperature of the hard disk. Even with the fan the CPU reaches 80C under full load so situation has not changed for the CPU and I think the problem is not CPU related.
EDIT: For comparison my Macbook Pro's hard disk shows temperature to be 38C and the machine has been on for couple hours and of course the disk is inside the case so those iMac HD temperatures seems really high in my opinion.

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