Well, there's certainly a few things you can do:
Switched caps are a serious problem. Get it wrong and you might spin a bearing in the first thousand miles. Check out these things:
1) The caps and rods have camfers on the big end. These camfers have to go towards the thrust side of the crank. Check to see if the camfers on the rods AND caps show this way:
Cylinder # 1,3,5,7: camfer to the front of the engine
Cylinder # 2,4,6,8: camfer to the back of the engine
Where two rods meet (i.e. 1 and 2, 3 and 4, ...) there is never a camfer.
Switch this and the uncamfered side of the rod will drag on the radius ground onto the crank where the journal meets the thrust face.
2) Does the crank spin freely without the rods installed?
If not, then of course you'll have to check your main bearings
3) Take the pistons out again and check if the caps match the rods visibly or not. You can probably see hone-marks on the journal bore. If these line up, you've got the caps and rods correct.

Check in this order and you should be OK. If you're in doubt anywhere along this line and you're not 100% sure that everything is correct, take the rods back to the machine shop and tell them to reface and hone them.

That's what I would do, but let's see whether someone else has any ideas...

Hope I could help you a bit,
Max