93 Probe 4cyl transmission install trouble after clutch replaced

I've installed many clutches over the years, and recently installed a new LUK clutch in my 93 Probe with 124K miles (replacing factory clutch).  I was able to remove the transmission without issue, installed new clutch kit, and had flywheel resurfaced.  When attempting to re-install the transmission, I just can't get it to slide in that last inch to mate with the engine!  I did not remove the intermediate shaft so I would have an alignment point, and it seems that something is stopping the intermediate shaft from seating... or the primary shaft/spindle from seating in the clutch and pilot bearing?  I have verified the clutch fits the spindle prior to install, and centered it as close as humanly possible using the included alignment tool.  I just cannot seem to figure out why it won't seat!  Is there something I'm missing or a trick to this?