Removing those excessive number of engines will increase the delta v. To decrease the thrust use the thrust bar. And I don't think you need those many on second stage. Either make a shuttle type launcher or just a simple 3 stage rocket, cause I don't think it's stable.
If you want to make a completely reusable 2nd stage you need ports, landing gears and also minimum 11% fuel for suicide burn.
And also only 2 RCS are enough for each stage