First thing to make sure is that the disk is centered between the flywheel and pressure plate. Those plastic alignment tools are junk. I use a quality metal alignment tool. Quarter Master sells them for about $50...
When I was younger, I actually didn't even use an alignment tool. I would snug the pressure plate just enough so the disk barely moved when finger pressure on the sides was applied. You would be amazed how well you can center the disk by feeling all around the edges and adjusting accordingly.
Never use bolts to draw in the trans. Even then everything is aligned, it may take a fit of fiddling to get the trans to pop in. I always have the trans in gear and have a spare yoke installed, so as I pus the trans in, I can also turn the input shaft. When everything aligns, it will pop right in, all the way...
Andrew
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