Hi mate, welcome to the forum.
Thats bad luck you've had there.........guess things can only get better

What happened to your old gearbox? Just because the mainshaft seal went shouldn't write it off.......easily repaired, or did you drive it with no oil?
Sounds like you have the timing marks all sussed out, however when you say 'is it ok for the crank pulley to move slightly', how much is slightly? More than half a tooth? Are you going in the correct direction with the tensioner? Usually you can get it pretty much spot on. There is also another mark you can use for the crank, although the fly wheel alignment is fine, you can double check with the pulley at the timing belt end........there should be a 'notch' that will align with an arrow on the timing belt cover.
Good luck and let me know what happened to your old gearbox.