You should NOT have had to do what you did!!! Also NEVER suck the tranny in with the tranny bolts. If its not going in YOU haven't done something right. Either the dowel pins that center the bell into the block are missing or screwed p somehow (I suspect this is your problem), wrong pilot bearing has been installed if you changed it, the clutch pressure plate isn't exactly aligned, the ring on the bearing retainer might have a nick or high spot in it, etc. NEVER EVER suck the tranny in or "beat" it in... I SPEAK FROM EXPERIENCE. Back when I was a newbie I installed my first clutch on my car. I ran into the same problems and didn't know any better and sucked the tranny in with the bolts. I didn't know it but in doing so I knocked out the center of the pilot bearing and proceeded to take out 3 mainshafts in my trans, I attribute this to a bent input shaft that "appeared" at the time to be OK. After a LOT of money and frustration I got it all figured out, but I truely hope for your sake that you didn't mess something up.
If the tranny goes most of the way in but is stuck at that last 1/4" or so, do what was said and hook up the clutch and have someone press the clutch pedal in and out a few times as you push the tranny in, this will let the input shaft of the tranny help center the pressure plate, this is in addition to centering the PP before hand with a clutch aligment tool which also MUST be used.
Also, are you using the stock bell housing? It also sounds to me like you may have a bell housing indexing problem which can cause all sorts of BIG problems. The center hole of the bell housing MUST be no more than .05" off center of the crank centerline. This is measured witha dial caliper and magnetic base and is EXTREMELY important when using a different bell housing from stock, or if the block has been align honed. I really can not stress how important this is, and I'd be glad to help walk you through it if you have never heard of this, or know how to do it... most don't.