As they've already said, but common issues:
1. Did you use the new custom pilot bearing for the 3550? Not a standard one.
2. Did you use the specific clutch disc for the 3550? It's not custom, but it's not Bronco.
3. If you didn't use the pilot tool, you could be pretty far off. Especially if you didn't monitor the position of the disc as you were torquing down the pressure plate/cover.
If you did all of those, and are pretty sure that the disc is close to being centered and you know the splines have started to engage but can't get the tip into the pilot bearing, you can connect the clutch and have a helper push down on the pedal to let the plate self-align while you're pushing in on the transmission.
This has worked every time for me, when the cheapy clutch alignment tool didn't.
Actually too, short of connecting all the linkage, you can actually push the clutch release lever enough to relieve enough pressure for the disc to float a bit and self-align.
I did it that way a couple of times when I was younger, stronger and more limber. Not sure I could still do it, but it does work.
Good luck!
Paul