Perhaps you could also explain why you need to run these, apparently, critical projects on three different setups?
Why the need to have the EXACT project worked on the SAME machine with 2 different versions of ST? With, I assume, both having purchased licenses.
Surely if you have purchased a license, you have already decided to use this software?
If then you are decided, why edit projects on the SAME machine with DIFFERENT versions?
If you are just testing the differences of the various releases, Linux over Windows or ST2 over ST3, why subject your important project to possible error by using untried software?
Having Linux an one machine and Windows on another makes much more sense, I can see why that might be a case. Stressing it with a LARGE project also makes sense.
However, by using this project to stress the software, it seems like you are deliberately setting out to push something to breaking point in an effort just to provoke a response. I hope that is not the case.
Add this on top of the already mentioned suggestions and re-examine your point of contention.
As to the size of your project. Seriously, 80,000 files?!
Surely that could be broken into more manageable chunks? I cannot imagine ANY project that would NEED access to that many files at the same time.
Your work flow would greatly increase if you could divide and conquer your project.
Putting aside any misgivings I may have over your intentions with these posts.
If you provide more detail about your setup perhaps ANY problems that may exist would have a better chance of being solved.
You mention you run ST2 and ST3 on the same machine.
Are they both on the same operating system, Win 8 64 bit?
If so are there any conflicts with the two versions with regard to the installed plugins?
Are there any conflicts with Windows DLLs and the two versions?
How did you determine there is a "indexing/ST processes" problem? What was it?
The more detail you give the more chance you will be aided. By just crying fowl all the time you are just, as was said before, acting like a diva.