Crack the bleeder open. I can't promise that it will help... I almost never do that but it can't hurt.
You are getting hung up on one of two things: the input shaft is just not quite lined up with the pilot bearing, or the input shaft splines are not quite aligned with the clutch disc. The slave cylinder doesn't have that much resistance, I guarantee one of those two things is causing this whole deal.
This part you're on right now is by FAR the hardest part of installing an RBV trans. I have had some just slip right into place, I have fought others for hours and then they just slip in. Keep at it, wiggle it around until you get it. I have found that it's easiest to just put the thing on my chest and bench press it into place... then you can kinda lay on your back under it and use your knees and hands to maneuver it around. Not the most fun thing.