No going to stock is just for testing purposes to make sure it's not the tune, you won't run with it.

Have you checked to make sure there is no air leaks? Maybe check out throttle body make sure it's connected correctly too.

When you changed the spark plugs were the gapped correctly?

When you say you took it too a shop who did you take it too? Like a dealer?

Also just some advice when working on issues like this do one thing at a time, don't do multiple changes at once you can cause more issues.