ECU can stay the same. You just need to trick the neutral safety switch harness from the auto trans into thinking you're in Neutral or Park. Basically you solder two wires together and heat shrink them, and you're done.
Rear drive shaft for the manual is a tiny bit longer (3/4"?). In theory, the shorter one can expand to take up the slack, but I've heard mixed things about using the auto shaft with the manual, so I bought a longer manual shaft for the swap I'm going to do.
I hear the front shaft is the same.
You need to swap the flywheel and flywheel bolts too. Bolts are different lengths.
I hear the trans crossmembers are the same, but the crossmember-to-trans MOUNTS are different. I bought a manual mount to bolt to my crossmember.
You also need the clutch line. Either the original type hard line and soft line combination that runs to the trans, or an aftermarket type. Original type is hard to find without a donor truck. I bought a stainless braided aftermarket, which means I'll have to do some hacky mounting on the firewall with some screw-in brackets.
There's some other trickery involved to get your reverse lights going again, to plug in the clutch start and cancel switches if you want them to work correctly too.