I'm going to attempt to swap the motherboards between my two (regular) New 3DS systems, because one is a Japanese version in black and I think it looks way cooler than my American white one. The only problem is that I cant find any real tutorials or information for board swapping on the "regular" New 3DS. If I were to make an educated guess, I'd say both motherboards are the same and I'm safe to swap em', but I can't confirm it 100%. What I need to know is if I'm safe to proceed or not, or if there's any other negative side effects that can occur.

there should be no physical difference between the jpn and na motherboards. only diffrance would be the region locking but thats it id say your safe to swap.

It's not as easy as it sounds. While sure it's not the hardest thing in the world, it's definitely alot worse then trying to do a GBA SP or a GBC for example.
From what I know about the 3DS you will have to take almost every screw in this thing out to get the swap done, however the amount of parts that clip together are what will cause the issues. Just make sure you take it slowly and be very careful on the disassembly.

The boards should swap so the only issue is doing it without damage or missing something. I recently swapped a couple parts on an original 3DS and thought I broke them due to a cable I left disconnected, missed during initial reassembly, couldn't see when going back over everything, and could find no mention of in the crappy guides I referenced. I was in a rush which definitely contributed. Just be careful, take your time, have the proper tools, and triple check everything!

Tweezers and toothpicks can be useful. Careful with the flat cable connector clips. If they are anything like other 3DSes, some latches flip away from the cable and others flip toward. I remember breaking one in an original DS 10yrs ago and I had to get clever to fix it without replacing the connector.