I just bought an SRT 6 about 2 weeks ago from today and had the same problems you're describing. Basically the discharge air temp was getting about 190-200 degrees after the SC according to my scan-tool. the ECM will look at that and say "heck no turn off that SC" and you'll lose all your power until it goes below 200 degrees then kick back on.. and turn off again.. etc..
Check Fuse 13 FIRST as it's an easy fix if that's blown. (Driver side) Fuse Panel.
This fuse brings power to the pump.
For me it was the pump. Super easy install took me 1 hour to do it properly. Johnson pump worked fine.
After install I drove around.. Smashed it a couple of times while recording IAT It stayed at about 90-100 and at max 115 then dropped back down..
Hope this helps!!
Edit: Here is the pump i got.
https://www.amazon.com/gp/product/B0...?ie=UTF8&psc=1