Yep...theres no hope now. I fu**** it up good. I dove into it this evening with the service manual and found the removal of the processor assembly was pretty straight forward. When removing both CPU's I could tell there was definitely some thermal paste issues, cleaned it all off and reassembled. Booted into OS X and CPU A was approaching 200F, much much worse than before, however, CPU B was in the 70 degree range (I should have just ran thermal calb at this point but I apparently was delusional). Thinking I botched something with CPU A I took it back apart and cleaned it and applied new thermal paste again. Once reassembled, I got instant overtemp LED and within a few seconds a checkstop light and a complete freeze. Just finished taking the entire assembly apart again and checked very closely for damaged CPU pins on the LB, but it all looked fine. Reassembled again and still got the lights. This thing is as good as a paperweight now...I really regret tearing into this. I've definetly learned my lesson. This is the first thing in my life technologically I just couldn't seem to conquer. Bummer.
You're fine. Sort of... Just stop experimenting with the ASD you're not doing any good to those cards in there with temps that high idle, yeek.... But... You absolutely need a rebuild on the LCS. There are small filters in the lines and those get gummed up and won't let coolant flow. The coolant in this stuff is nasty. Checkstops and overtemp leds were my hell. The fan speeds are responding directly to your core temps. Fix the core temps and your fans will respond accordingly.
You took the LCS out and that could have shifted things and now either a pump has failed or the clog is worse. I'm thinking clogged up.
I have this exact model. Dual pump stock and everything. It's impossible to successfully rebuild it IMO. I tried it and filling it is one thing, then bleeding air out of it is a nightmare. Not to mention getting into it with all of the epoxy... and getting the lines off requires cutting. Each processor has a separate chamber which makes it harder. If you want to try and rebuild this unit, keep the existing tubing on the lower half and get a way to flush it real well. Still don't recommend tho. Junk it and keep the pumps for backups.
With mine, I bought a single pump version off ebay (others are right in that they're all lemons. Finding a good unit I don't think exists because of their age) Went through this bad pump fiasco already and had a not-so-pleasant chat via ebay for weeks. finally got refunded for a bad LCS.
I refurbished a single pump version with great success. Temps hover around 35 - 40C (95 - 100+/- F). Careful with the pump tho... they can get stuck on max rpm. The following guide has a pump refurbish as well. If that happens check out DIYINHK DDC pcbs
You rebuild that LCS, you're golden. Even if you get it to pass thermal cal your fans will still be high rpms. I can tell you need a rebuild because of the temperature disparity between CPU A and CPU B Mine had the same thing. Only the other way around. This guide:
http://www.saunalahti.fi/~holindho/g5-quad-v1-lcs-repair.html is amazing and a huge help.
I have a whole bag of the special O rings for the cpu block if you end up going this route. Happy to send some your way.
Also, toss the black plastic shield thing you have around the cpu dies. Thermal paste gets in the gaps and acts like an insulator. This doesn't help your situation.
Here's some pics if you're interested:
http://imgur.com/a/P8QKX AND
http://imgur.com/a/3I7Cg
I spent this last summer getting one of these in prime condition. Lemme know if you have any questions