1) there are 5 screws/hex nuts what ever. If you fully tighten 1 screw without doing any other screw the heatsink will be lopsided and never correctly mate with the cpu. So the safe way to do it is ;
a quarter turn on one screw upper left (1)
then a quarter turn on the opposite screw lower right (2).
then a quarter turn upper right (3)
then a quarter turn lower left (4)
then a quarter turn on the far left middle(5)
doing those 5 screw 1/4 turn would be one rotation.
repeat all 5 again 1/4 turn two rotations.
this is tedious and takes at least 5 or six rotations of a 1/4 turn, but it is safe! it will result in an even mating of the heat sink with the cpu!
2) if you install the cpu and you were using the oem stock fan controls the system should just keep doing that. I just like to use iStat I was a long time mac mini user and did not like the osx fan controls on the mini.
IF YOUR HOME IS HOT AND IF YOU REALLY PUSH YOUR MAC PRO OSX FAN CONTROLS ARE NOT GOOD ENOUGH! This is my belief my opinion. Many people agree with it. This would be true with the stock quad as well as the hex mod. Both pull the same juice(watts). Both have the same max heat specs.
3) Not to my knowledge
4) I have a fully updated mac pro and the hex 3.2 still works for me. I keep a second osx always one update less then current. Just in case that happens. If it does I will be talking about it.
5) you asked in another thread about artic silver
http://www.amazon.com/gp/product/B001FVI91U?ie=UTF8&redirect=true
I used this kit. I used the cleaner on the old cpu then the prep. I then sold the old cpu on ebay for about $200. I used the cleaner on the new cpu then the prep.
I then squeeze out some on the new cpu and used my gloved finger to spread it evenly. I have done this on more then 100 amplifiers That I built for music.
The instructions don't say to do it. they say make a lump in the dead center and when you tighten the heat-sink the artic silver will be spread.
Their way is fine I am used to my way and it works for amps because many heat-sinks are far less precise then the mac pros.
Remember somewhere in this thread I mention I have only done 1 cpu upgrade and this is it! I have done hundreds of ram installs hdd installs case mods and many audio amps and speakers. I can solder and have a decent background in electronics all self taught do to being color blind (not complete just partial).
Most trade schools will not teach color blind people electronic repair. At least this used to be true in the 70's and 80's.