I have a stock 04 Civic EX. With 250k miles on the car, I just blew a head gasket. To add insult to injury, the transmission went out at the same time. I'm the 2nd owner and I'm assuming the transmission was already serviced or rebuilt at some point. It would be a miracle if the original made it that far.

A friend of mine who's an experienced mechanic is swapping in a low mileage USDM stock engine. This new engine came out of an 05 Civic EX with a manual transmission. Mine is an automatic.

1) Will all the connections from the new engine work with my transmission, or will he have to modify the wiring harness, etc?

2) I'll probably get the transmission rebuilt the right way with an over-sized cooler and in-line filter. Of course I've read about the problems with these transmissions, so has anyone had any success modifying them so they're significantly better than stock? I had a 90 Accord that went 325k miles without even changing the fluid. Any way to recreate that in these Civics?