You have an issue with cooling due to lack of space.
You have no problem with framerates or fps really when left at stock
You then mess with it and expect ti to be the same idle as stock and are again worried about temperatures?
I'm sensing a pattern here.
If temperature is really such a big deal you need to case your case to allow better airflow or just leave it alone and keep the filters/fans/rads clean as to maintain the same cooling ability.
There is no magic fix here you have done all you can without changing things.