Is there a way to do a transform then remove all line items except for specific ones (I have the ones I need in a list). I don't want to do some crazy inner loop to test each lineitem against each ID in my list).

Doing a transform and then doing the compare seems like how you'd want to do it. Otherwise you'd have no idea which items to remove so it makes sense.

From a big O perspective, its pretty inefficient with that inner loop.

Sure if you have a million lines. Otherwise, it doesn't matter