01 mustang V6 shut off wont start

I have the pipes pypes Street-Pro Dual Cat-Back
Exhaust - Turn Down Tips installed on my 01
mustang v6 and also installed the Flowmaster
Super Flow 44 Series Offset/Offset Oval Muffler -
2.5 in. When installing i cut off the muffler that
came with the exhaust system and placed the
flowmaster on and held it together with clamps.
Doing so left a small gap on the tailpipe end of the
muffler which i fixed with a VersaChem Exhaust
Repair kit. Recently my muffler came off and the
only thing holding it on was the tailpipe. I repaired
it by adjusting the muffler so the clamp had more
to grab on the front end and sealed the remaining
gap on the tailpipe side with the exhaust repair kit.
After doing so my car had a faint repetitive
thumping noise coming from the area under the
car thats below the radio (maybe slightly forward)
when i acclerate and slow down. I pushed it off.
The noise got deeper and my car shut off. The
service light came on i ran the code and got p0230
ended up replaying the fuel pump and got the car
started again. A few days ago i was driving the
same deepend noise occured so i pulled over my
car lost power and cut off. This time there was not
a code. The fuse is good and the fuel pump was
replaced less than a week ago. I cannot figure out
what the problem is please help