Ok everyone quick update for you:
I have good news and bad news.
The clutch arrived and low and behold, a Centerforce Dual Friction clutch is merely a LUK clutch with the weights added to the pressure plate and one side of the stock organic LUK disc taken off and Centerforce's ceramic material with a gold plated backing riveted on. To be honest, I feel kinda ripped off, but it is what I had when I needed to finish the project.
That being said, I love the clutch. Extremely easy pedal, smooth engagement, seems to hold strong, albeit the ceramic is a little loud on the flywheel.
I also got a throwout from the local dealer, looked way better than the one I had, as well as a pivot ball stud. I also got a bronze pilot bushing from Napa. Overall, I am very pleased with the clutch although I could have probably just gotten a much cheaper Luk and had the same results.
Now here is the issue, and my need for more help!
Rebuilding the tranny was not too bad. For someone that NEVER gets a project done when they plan to, I actually finished this project in the week I had off. A local shop had a press and he let me use it to remove the bearings. Like you said tanman, I ended up cutting some off.
I bought a cheap rebuild kit from the big auction site which was sourced from the Transparts warehouse which included the fiber lined synchros and bearings.
Here is the problem: Although the bearing grind seems to have disappeared, I have A LOT of gear rattle, especially when it warms up. It rattles at idle noticeably, and it really seems to rattle/groan/growl in 3rd and 4th, at low rpms, although this is probably more because its the most torque at the lowest rpm (besides 5th which I am never in unless I am moving fast enough to not hear sounds). Here are some important things that I want to point out and maybe you guys can come up with some suggestions:
1) Definitely coming from inside the gear case
2) Replaced input bearing, however, I DID NOT check endplay in the mainshaft or anything for that matter. I simply reinstalled the existing shims (two for the main, two for the counter)
3) DID NOT replace the input shaft, although it has grooves in it from a damaged bearing. I used a pilot bushing, see next point.
4) Pilot bushing was TIGHT on input shaft. I had hit the input a few times before I purchased a good puller to remove the input bearing, which mushroomed the end a little bit. My dad when he was helping me smoothed this out some with a file and pipe paper because with the first attempt to install the tranny we could not get it pushed into the bushing.
5) The second attempt to install the tranny yielded the same result, however with only the length of the bushing still to push in, we were able to pull the tranny to the bellhousing using the bolts, with NO SIGNIFICANT force. A little effort with a regular wrench and the bolts pulled the tranny right in. I know, not the way to do it!
6) When installing the fifth gear nut, I used an impact with a socket I customized from a chain store. I locked the tranny in two gears at once to do this and torqued it as far as our impact would move it (130 ish psi).
7) When assembling the mainshaft assembly, I had the WRONG oil, thanks to the dealer. It was synchromesh. Not knowing until after I had the mainshaft together, I used this oil to moisten the new fiber lined synchros as I was putting it together. After realizing the problem, I went back to the dealer, returned the oil I did not use, and purchased the right (expensive) fluid, which it is currently filled with.
8)The noise goes away when I depress the clutch pedal.
9) I had a shop manual for my truck, which has an nv4500 section in front of me the whole time. I do not think I assembled the mainshaft incorrectly as I had the diagram in front of me the whole time and the synchros are angle and notched to only allow assembly one way.
10) I am 95% sure it is not the clutch.
11) Almost forgot, I did chip 2 or 3 teeth on the large gear at the end of the mainshaft using a puller before using a press. It is the very last gear on which the rear mainshaft bearing is installed. It is the reverse gear (cut opposite the rest). This is the only gear that has damage.
Please read through these things. Is there anything that jumps out at you? I am leaning towards input shaft in pilot bushing or not checking the endplay (it seemed tight but that means nothing). Please, any and all thoughts are welcome. It looks like I may be removing the trans again when christmas break comes around.....
Thank you everyone for your help so far!