I've unplugged injectors a thousand times at least and never once had them pop in the intake.
That also contradicts your original post.
No matter what that engine should start on a bone stock tune. It sounds to me like something may have happened to the engine. If it ran fine before, now it won't start and it's backfiring either out the exhaust or in the intake, that sounds like it broke a timing chain or some other type of valve train failure.
Check the codes. Don't know if you ever mentioned you did or not. If there's a cam sensor issue it'll make them hard to start and they make funny popping noises when they don't start. But typically you can cycle the key off then back on and they fire right up.