If you're going to do the swap....here is my take on what you've disclosed.
You do a lot of driving for work. That EJ257 is going to be a PIG on your wallet. I'd go EJ207.
If you upgrade the tranny, get the JDM 6MT....just a touch stronger with steel shift forks and better matched ratios.
If you go EJ257, go with the USDM tranny as well, you'll get better cruising ratios for the highway...
If you go EJ207, go with the JDM tranny for some fun, along with a bit of economy if you want with the smaller displacement.
You're either going to have to splice, or go insane converting all of your cars connectors to transplant another cars harness entirely. If you go to a well known shop, you'll pay, but you should get in return, some well done work, taped, loomed and tucked away like the factory.
You don't want to worry about the motor? don't even think of piecing the motor together (aka Frakensteining); go with an off the shelf complete long block at the very least.
Thats my quick take.