The transmission and flexplate get ditched for the new manual and clutch assembly. The front cover for the manual t-case has a lip on it for lubrications (autos don't because they "bathe" in ATF), so that cover needs to be changed.

The interior pieces aren't cheap, when I converted mine to 4x4 (stayed with a 5 speed) I still was stuck spending $200 on interior bits because they were impossible to find in yards. As for the clutch hydaulics, there's a spot on the firewall for the master cylinder already and a through-hole for the linkage. Find a donor truck and get all the parts from one truck. The ECUs are different, you will be abandoning the transmission harness and I do not know if the rest of the wiring is the same (and I don't feel like looking it up right now).

No driveshaft differences.

Don't expect a gas mileage increase, as the autos have a taller overdrive for highway cruising that tends to make them more fuel efficient.

I'd consider a swap like that similar to my 4x4 conversion, if you are going to keep it a long time and are going to heavily mod it out (to make trading it in a waste), then it might be worth it if you get the parts at a good price.