* How much engine oil does this thing hold?
10 quarts of oil, assuming you use the original oil filter. It is possible to use a filter from a Powerstroke in place of the original filter, without any modifications. It'll be a somewhat tight fit, but it'll go. This will give you an extra quart of capacity, and extra filter area.
*How much trans fluid should the 5spd hold (and what is recomended to put in it?)
I'm not sure on the capacity, but the ZF5 uses automatic transmission fluid. IIRC, gear oil will shorten its lifespan considerably.
*How much oil should the rear end take (regular 80w90 gear oil is OK for that?)
I'm not certain. You should have a Ford 10.25 axle, and all of my books only cover the Dana axles that were standard equipment before mid '85. The Dana 70 holds 6.6 pints of oil; I imagine that the Ford 10.25" will be similar.
*How much coolant does this thing hold? (I read some where on hear to get the Cat long life antifreeze as it has all the additives, is that correct?)
The 6.9l holds 29 quarts originally. I think it's a safe assumption that the 7.3l is the same. Re: Cat antifreeze, there are reports out there that it'll eat oil cooler O-rings unless the O-rings are fairly new. I did a top-end rebuild on my engine last summer, and also replaced the oil cooler O-rings...so I decided to switch to the Cat antifreeze, and I've been realyl happy with it thus far. BUT, based on the reports mentioned above, I'd be wary unless the O-rings are recent.
That said, whatever antifreeze you use, you should get a low-silicate antifreeze, and then get an additive known as SCA or DCA. Ford sells it; it's known there as FW-16 (or at least it was; that may have changed). This additive will help prevent cavitation.
*I got my axel code off the door as "35" so I know I have the 4.10 gears in it, any idea if they came with a limited slip or anything fancy like that?
Limited slip was an option, but it doesn't look like you have it. I'm not sure what Code 35 is (again, all my books are for Dana axles, and the Ford axles use different codes), but if it had limited slip from the factory, the first number would be a letter instead. For instance, the Dana 70 (with limited-slip) in my truck is Code G2. The code for the exact same axle, but without limited slip, is 72.
I don't think there's anything critical that you need to know in the diesel supplement, but someone else may be able to answer that better...I've been around diesels enough that, between the prior knowledge and what's on this site (and the site that pre-dated this one), there wasn't anything I needed out of the supplement that I didn't already know...even though I have it sitting here *lol*
Re: the clutch, not sure if '87-'91 trucks have the same problem that '80-'86 trucks did, but on an '80-'86 truck, that can be the indication of a cracked firewall. The firewall wasn't built as strongly as it should be, in the area where the clutch master cylinder is. When the firewall cracks because of too much pressure, the pedal will become harder to push down and you'll get symptoms as you described. Another possibility (actually, this one is supoprted by the pedal not wanting to come up all the way) is that either you're right and the clutch hydraulics need to be bled, or the master or slave cylinder's on its way out. Hopefully the hydraulic system's okay; bleeding it out is a cast-iron PITA!
The clutch master cylinder is just to the passenger's side of the brake master cylinder, and there should be a rubber diapharam covering the resevoir when you pull the cap (standard screw-on deal). The diapharam's deep enough that it'll look like you're looking at the bottom of the resevoir. Pull the diapharam out before you put brake fluid into the master cylinder; otherwise it'll sit in the diapharam, make it look like the system's full, but won't actually do anything.
Hope that helps...good luck! And the front end of the truck looks nice; I imagine that the bed and cap will clean up just as well...