You have a windsor or romeo?
Heres where I am at relative to your list. I added a couple little things and asked a few questions...
PM AMstanger to get your American Muscle dicount code if you end up buying a load of stuff from them like I did. They are a great company.
shifter - Bought MGW. Also their inner dust boot. $197 shipped.
manual pedal set - Bought a nice 03/04 Cobra pedal box on ebay for ~$150
clutch cable, quadrant, adjuster - Bought cable, quadrant and adjuster for $100 American Muscle
manual shifter bezel - Dont think this is a must. one guy re-used the auto one. Either way its a cheap part.
Leather shift boot - Bought from American Muscle. $50
shifter base insulator - Lower Shift Boot / PLate was about $50 new. ebay.
shifter handle - Ford Racing shift knob from American Muscle. $40 ish
shifter gasket if you dont want to use silicone. $10 at American Muscle
engine separator plate - Whats this???
pilot bearing - Bought Ford. American muscle. $10
clutch kit - Bought RAM HDX from American Muscle. $250
flywheel - Bought Spec Aluminum flywheel. 6 bolt. Open box $250. Looks like a nice piece. Replaceable friction disc.
flywheel bolts - Came with flywheel
pressure plate bolts - I think these came with the flywheel. Has a big bag of hardware.
trans - T3650 Ford factory re-manufactured (all TSBs done) $950 shipped.
trans fluid - Need to re-read that T3650 thread and buy the right fluid. Rave reviews for royal purple...
http://www.americanmuscle.com/royal-purple-synchromax-manual-transmission-fluid.html
trans sensors - ?????
shift fork - Ford OEM shift fork kit. $50 bucks new.
x-member if going t56 - Does the stock crossmember work with 4R70w and 3650 then? I dont need to change mine? I think the crossmember for 99+ 4r70w and T3650 are the same. Need to confirm at the Ford parts counter.
manual trans wiring harness - This is where I have to most questions.... whats different about the harnesses? Do we have to replace (~$160) or can the auto harness be modified slightly? Also how is the stock ECU going to react. The other guy that did this swapped his ECU too.
driveshaft - Bought Ford Racing aluminum DS from American Muscle for $300
or can just get a 5spd yoke for your stocker for about 75 bucks. Steeda.