Either something is wrong with the new bottom end, or problem with the assembly of the cylinder to it.
Was xyl and head retorqued after hear cycles? Engine leak tested after assembly?
All suggestions thus far are pretty much spot on. Arguing about whether or not to do them will get you less further help.
It's all a process of diagnostic elimination. As are asking questions about your set up, and what you have or haven't done or tested.
Are ALL electrical components the ones from the engine that did run?