1. Alignment tool = critical.
2. Carefull handling of transmission, do not let it hang!
3. Alignment pins for trans, good idea, I use them also.
4. Put it in gear and wiggle the output splines as you manuver the trans into position.
5. Start over, check the disc on the input shaft splines from both directions. If you have a minor burr, you can touch it up with a file, no problem.
If you start over, check for those small dowel sleeves on each side of the adaptor plate, these align the centerlines, very important parts.
DO NOT use bolts to force it in, only causes problems, bent disc, possibly even drives the pilot out the back of the F/W, yep, fixed one of those already.
Patience and skill, not force.
Good luck.