Replacing trans and motor on 1 car is bad idea.
It depends on the seller and the shop who installs it. If you want some sort of warranty on a used engine, be sure get that in writing. Make sure it includes terms acceptable to you for both parts and labor. I’ve never gone the used engine route myself, but I think its pretty common for a used engine to come with a warranty, one year or something like that. The engine seller will know quite a bit about the engine b/c when it came into their yard they’ll have started it while it is still installed in the junked car, listened for weird sounds, tested compression, diagnosed any engine codes, etc. So its very unlikely you’ll get an engine that is toast from the get-go. Choose a shop that has done this sort of thing many times, then they’ll know what to look for when finding an engine for you. The don’t want to have to repeat the job, so they’ll be extra careful, esp if you insist on a warranty. Once it is installed and they say its ready to pick up, good idea for you to make sure the check engine light turns on w/the key in “on”, engine not started. Then it turns off immediately after starting the engine. Take it for a test drive with one of the shop staff with you to make sure it drives to your satisfaction, then when you get back to the shop ask the staff to prove there are no diagnostic codes stored in the computer memory.
You can also use the forum search feature to see what other have said about used engines here, link upper right this page.
I had something similar with my jetta, P0305, 5th cylinder. Dealer kept changing plugs which only delayed fixing and costing me $$. Once we changed (all) the fuel injectors, problem solved.
This is a pretty good article on diagnosing p030x misfire codes.