Looking through the forums on various car sites, I read over and over again that one of the biggest causes of disappointing results is to replace panels, paint them and then hang them on the car with the notion that they will fit like they should.
The advice I read from those who have done this a few times before is to assemble the entire car before blocking and sanding out the body and after a great deal of time is spent making panels fit just so. I really get the importance of test fitting parts because even original parts between cars don't fit the same on a different car. You don't want to be adjusting newly painted parts to set gaps.
My question is about the mock-up phase. Does one need to have the full weight of the engine and transmission on the body in order to get these things adjusted just right. Or can you get by with mocking up the body without the engine and transmission installed. Does the engine weight effect body gaps much or is that a minor concern?
Mock-up, mock-up, mock-up. I end up assembling and disassembling a few times before things get 'tightened down'. To answer your question, the engine and trans being 'in or out' doesn't effect the gaps. If it did/does then there's a problem.
If it were me, I would take all the sheet metal off, have the Jambs done on the shell, and paint the inner lips of all the panels and THEN mock it up til you are satisfied with fitment. Then take it to the shop and have it painted. The finished product will not have the little tell tale gaps where you can see another body color inside it.
I always mock before ANY paint is laid down. It gets you familiar with this particular car and it's fitment issues before you start spending money on 'color'. You can mess up your edge and jamb paint on the first mock up.