Cakey, unless your description of events so far is accidentally ambiguous, I think you need to take a step back here.
If I'm teaching you to suck eggs, I apologise, but I wonder if you know how to use plastigage? It's purpose is to indicate the amount of wear (in this case between rod bearing and crank journal) that currently exists, and that figure when arrived at determines whether it is in acceptable tolerances to fit standard size bearings or oversize ones, the latter requiring a crank regrind. If you have just blindly ordered new bearings without checking this first, then I would suggest you do it now before you end up with a set of new bearings that are non-returnable. You could well be ok, but better to check now than find out later.
That rod cap in my opinion is distorted. The gap will be more evident with the new bearing because the old one will have taken on the shape of the cap to some degree. Caps are usually matched to their rods, so I suggest you find a good rod/cap to replace what you have. If the previous measurement of bearing to crank was favourable ie no regrind needed you should be able to use a new rod (are they available?) but if you opt for a used rod check measurement again to ensure it is compatible.
You can fit the pistons after the cases are back together - indeed this is preferable to prevent damaging your pistons. But don't worry about this yet, you are getting ahead of yourself.