Not turning over N47 - after doing timing chain R60 Countryman

My Mini isn't turning over after I removed the engine and timing chain.

Starter was smoking.

However once or twice it turned over just slowly(battery was likely not at 100%)...and I can tell it turned by where my timing marks were.
I am positive the timing chain and everything went back on ok. I was able to easily turn the engine over by hand and turned it a number of times and timing marks lined up perfect.

Questions:
1) Any initial suggestions on what it could be ?
2) One thought is that when I took the slave cylinder out it was fully extended and I just pushed it back in place to put the bolts on etc... I understand air can get in ? If that is the issue does anyone have any suggestions ?
3) The transmission came out with the engine and it went in fairly easy -- about 90% of the way on before tightening bolt - but could something have jammed - such as input shaft and that is jamming flywheel ?

I am leaning towards the slave cylinder having an issue and not releasing the clutch when starting - anyway to check that ? I bleed it - even though I understand that since I didn't open it up it should be out. I believe though that since the bleeder is before the end that extracts that the fact it opened all the way up means there could be air in the end bu once again I am not sure how to know.

Any advice would be greatly appreciated..already put way too much money and time in it.
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