if i got a flowmaster muffler and had the rear resonator removed, on a single in single out exhaust would the change in backpressure mess with the mds

 

I did the exact same exhaust you are talking about: removed the resonator, welded in a flowmaster 50, left it SISO. Not only does the MDS still work perfectly, but no check engine light, better gas mileage, and definately no degredation in performance.