Alot of things to answer. I can tell you wiring.
1) Use cat5e for your network wiring.
2) Wiring under the floor? Flat wires? Try this product line:
http://www.flatwiresolutions.com/index.html
Now for the actual wiring for a home theater:
You will need:
-14-4 speaker wire (16-4 will work as well) if you are planning to bi-wire/bi-amp your speakers. You need to run them from the receiver/amp location to each speaker locations.
-How many sub do you want to use? We usually use RG59 for the subwoofer run. Just use 1 run of RG59 for each subwoofer location. It gets abit complicated. This will only work if you have an LFE input on your sub. Otherwise you will need to run a 12-2 speaker wire for other subwoofers. Research your subwoofer before you decide on which wire to run. You should also provision a single CAT5e for control of the subwoofers just incase you have something that doesn't do auto sensing.
-you might need a dedicated power outlet for your subwoofer, you will need to ask the electrician to do this for you.
-Video runs from the receiver to Projector: You will need a long HDMI cable. Well it all dependes on the spec of your receiver and projector. As you mention you want your computer to work with your projector. Well there are plenty of scenarios here. I don't know your budget but here's what you can do:
-buy a video card for your pc
-buy a receiver that upconverts to HDMI. (Pioneer VSX92 for example)
-Buy a projector with HDMI in.
Now for the wiring (the safes thing to do):
-1 HDMI cable
-1 VGA Cable
-3X RG59 (component or s-vid or composite video)
-2X Cat5e (for control)
-you will also need a dedicated power outlet for your projector, you will need to ask the electrician to do this for you.
-If you are planning to have a motorized screen:
You will need 1 control cable, 1 power cable (18-2 cable)
Ofcourse you will need some interconnects for your AV sources to the receivers.
Regarding the tools: You will need a CATMASTER for your networking. Punch down tools, crimpers, a dry wall saw, ir emitters, etc. I'm not sure what are you planning to do.
There are people who does this professionally. You may want to consult your local custom integrator company. A typical home theater would cost you around $30000 and up. Of course there are people who claims to be able to do it for less. Hehehe by using cheaper components though. Expect a higher labour rate for it seems that you are doing a retrofit.
If you are interested in a home theater (we are in Toronto, Canada)...I can point you in the right direction...but you have to guess my email...hehehe won't post it here. Too many spammers.