I need some suggestion since this is the second time this happens when the built engine goes back in.

After a lot of cursing the mating was successful (one of the guides usually misbehaves), and then all the fighting with the AWR mounts (softest bushings this time).
So when tightening the gearbox and starter up I just tried to turn the engine by hand to verify and it's stuck.
Loosening the gearbox+starter just a little makes it turn just as it was in the stand.
The clutch pack is a SuperMiata single race clutch and I never had this problems before we build the bottom end. 5speed with Mazda semi-straight gears and a 02 block.

I don't remember if I left it loose last time or tightened it after some minutes of running (the current plan for tomorrow (some hours of wrenching left before startup).

Is something just misaligned and it will shake in place or is the gearbox input shaft bottoming in the crank (but wouldn't that require the thrust bearing and oil pump to be terribly wrong)?
The stock engine I use for inspections just falls in place on its own now so this is something specific to this engine (same clutch was use before it was built and I don't think I had this problem then).

 

Check the pilot bearing alignment in the flywheel. If it's out, the input shaft presses up against it, doesn't press onto it, and nothing will turn.

 

Thanks for pointing out what I've missed.
The pilot bearing was installed flush but could be tapped in another.05" or so.
Now it's back in there and I only have to fight with one dowel pin and the pesky engine mounts.