ya know i had similar issues when towing ,but it was with my centrifical s/c wich in theary shouldnt have done it.i havent had a magna charger but from what i know they run out up high so i dk if thats the solution for ya .now heres what worked for me .i installed a larger cfm centr,s/c .what i mean is i went to a 1500 cfm from 1k cfm centrifical.i went from vortec sc unit to a paxton and its a night and day diff.up high down low ets all over.so my thought is maybe a larger turbo might be the answer.my 2 cents.but it worked for me i was super impressed and i had the same problem towing my 28 ft trailer.
mods:2004 sierra ext sb,20s ,big brake kit w,hawk pads,air bagged,2006 6.0 lq4 swap,vortec supercharged10psi, air to water intercooled w/ dual electric fans on it ,snow meth injection kit,60lbers, e-fans ,big radiator swap ,cam 218 /222 548/550 comp .hardened prs .1.85 comp roller rockers ,guideplates ,crane double springs,trans 4l65e built .pacesetter l/ts true duals w/x pipe and magnaflows,14 bolt rearend swap ,3.73s,aroemotive fuel pump system w/elec.fuel controller and bypass regulator a/n fittings, taylor 10.5s interceptor gauge,aem w/b a/f ,autometer boost/vac NELSON 93 OCTANE TUNED .