Your title should be "Unexplained Limp Mode after crash/repairs", especially if you can get the same problem running stock, or even in valet mode.
My guess is there is a leak somewhere in the system... I would check the intercooler piping as mentioned above.
Where you able to pull the codes on the limp now that you replaced the fuel pump?
Good luck, and sorry about the wreck... I am sure it will be good as new soon!