I first went to NAPA and got a LuK clutch kit. After me and my buddy got everything out of the way and wrestled the tranny out we took what looked like a dead crow (the old clutch) out and took the flywheel to have resurfaced. The machine shop told me they only took 20/1000's of an inch off, honestly i'm really not sure if that's a lot or not. I asked them if they thought I should get any shims for the difference but they said they didn't think it would be necessary.
The next paragraph is where I think we messed up....
Once back on the job we torqued the flywheel back down to 35 lb in a three pass star pattern which is what I read on a forum to tighten them to, (I later read that it actually was supposed to be 35 and another 1/4 turn, I'm not sure how much that other 1/4 turn will make of a difference) and then used the alignment tool to put the clutch and plate in, which was actually weird because instead of labeling which was the flywheel side this one was just labeled "made in south africa", but we compared it to the old one in the way we took it out and that's the way we put it in.. here's hoping that was right...
My buddy actually put the throwout bearing in because I was tending to another matter elsewhere in the car. We then wrestled the tranny back in so we could bolt it back to the engine... however once there we were having a problem getting it completely flush against the engine. There was around an inch of a gap between them and we couldn't figure out why we couldn't get it any closer. While he tried to push it flush I was on the other end turning the crank hoping that anything that wasn't lined up would do so and the tranny would then saddle the engine. By this point it was late in the evening and he had to be getting to work and was probably very frustrated. I too was frustrated but it's my car and I'm getting free labor so how frustrated can I really get? 
Anyway, after he left I called another buddy up, an older guy who has worked on cars and at car shops since prob before I was born. While I was waiting on him I tried to figure out what was keeping it from flushing against the engine when I thought to move the clutch lever. It was sitting more forward (towards the engine) so I moved it back and then went and turned the crank some more (maybe a millimeter or two, barely anything) and then went and tried to move the tranny again and it actually was able to sit up against the engine smooth. I'm not sure if it was the lever or turning the crank that did it but I was glad it was on. My second buddy got there and helped me start running the bolts and putting the mounts back on. Which by the way remembering which tranny bolts go where can be a pain in the
as some are longer than others. I do remember the two 17mm went up top but the rest are 14mm and some are longer than others as I soon recalled when I was trying to tighten the one up in the back by the axle and it bottomed out with the washer freely spinning.. Anyways, after we get the bolts back in and the crossmember and the mounts and all that I go to bolt the slave cylinder back on and the silver inside part is sticking out (I guess we'll call it a piston, not sure what it's actually called) So I started trying to force it back in but there was no budging, or very little anyway but as soon as I took my hand off it would pop back out. Now earlier I didn't mention but when I went to take the driver side axle out I disconnected the brake lines. I didn't want any pressure holding on them as they hung and it seemed easier to bleed the brakes than to take the caliper off and have to deal with mashing that back in. I'm not sure if this was a good idea or not because I later found out that the brakes and the slave are ran off the same reservoir, which I guess means they would hold the same pressure.. but I'm not for sure about that or not. But if they are and I'm gonna have the bleed the brakes anyway I figured screw it and I'll just bleed the slave too. So I took the slave cylinder off and mashed in on the silver piston which shot brake fluid everywhere, but nonetheless, once mashed in to the point of what feels like bottom'd out it still isn't far enough in to be able to bolt up to the transmission and have the push rod be able to sit behind the clutch lever.
So what would this mean? Does anybody have an idea? I mean sure I have my older buddy helping me but even he admits he's never done any work on a vibe. I listed all the things I think I could have done wrong so hopefully if there are others of you who did a clutch job you would be able to tell me where I went wrong. If there is anything I did wrong I would rather take the whole thing back apart and do it again the right way than just force it and have something go wrong in a couple thousand miles. Even if everything is ok but the flywheel actually really needs that other 1/4 turn then that's reason enough for me to take the tranny back off and tighten it again. I don't know if the clutch was put in wrong or the throwout bearing was put in wrong or if it's just a bad slave cylinder (which I'm going to post a pic of so maybe you can eyeball it and tell me if it should be in farther than that or not) but any help would be EXTREMELY appreciated more than you may know. Thanks in advance!
And because of work and school I won't be able to fool with it until sometime late this weekend, but if I do end up figuring it out I'll be sure to post.
Ok sorry guys, those pics are a lot bigger than expected.. Apparently picture quality and resizing and such is not my strong suit..
Wrestling it in and out was definitely a pain,