I recently swapped a 3.0l engine into a 2.6.
The transmsisions for the 2.6 engine cars is the 722.4 - really meant for a four cylinder.

The 3.0l engined cars came equipped with the much stronger 722.3 transmissions.

The 722.4 transmission will suffice for the 3.0l engine however you should drive the car with a a bit more conservatively .

The engine changeout job is not that hard - especially when you remove the transmission with it. As long as you can wield the spanners effectively the job is relatively straight forward. You will need an engine crane and adjustable leveler.
I managed to change the engines without losing the AC gas.

Change the front engine mounts out when you do this job.

However I.M.H.O. ..........an engine change out may not fix your problem symptoms as described. Depends on how complete the spare engine is......Plugs, leads, distributor, rotor, injectors, IACV, etc, etc, etc.

Old fuel filters can give the symptoms you describe.

The real reason I would change out an engine is that the head requires a rebuild.

Check the inlet ports of your spare engine and make sure they are not carboned up.