Welcome to SpeedSolving! You've got a pretty good start if you're averaging ~40 seconds after only a couple months, nice work. To answer your question most people don't rotate their cubes before PLL and instead simply do a U, U', or U2 turn to Adjust the U Face (AUF) to the angle they need for the PLL they have.
For example, take your cube and do U2 R U R' F' R U R' U' R' F R2 U' R' which is U2 then the standard J perm alg. What I'm assuming you'd do in this case is U y2 to "get your cube in the right position" then do J perm. However, instead of rotating what you can do is U' to position the last layer, then do J perm, then U to "AUF". This is what most people switch to as they get faster.
This is sort of hard to grasp when you're first learning, I certainly did what you're describing when I was first learning PLL and even still sometimes do in certain cases. The important part to take away from this is you don't need to align the blocks you use to recognize PLLs with their sides; learning to recognize them simply by looking at the last layer can take some time but will ultimately help you get faster in the long run.