Since I'm not shooting a Marlin in .45 Colt, I may not be much help, but a couple of ideas come to mind. First, I figure that the SASS guns are HUGE fun, but only when loaded as they were intended. . . .which means that the noise, recoil and power are matching the blackpowder loads, or coming pretty close. This is not the fastest way to shoot, but I enjoy it the most.
Sooty cases usually suggest that a chosen load is not expanding the brass enough to make it fill the chamber, which could also be causing the blowback you mentioned. The load should be double-checked with the manual and see if you can safely increase the powder a bit. Trail Boss is good, but not for everything.
I have gotten some of my loads from an excellent reference book, Action Shooting Cowboy Style by John Taffin. He specifically tested the 1894 Marlin Cowboy .45 Colt using VV-N-100, Red Dot, Tite Group, WW-231 and Unique; bullet was the Bull-X 250. His accuracy was not very good, IMHO. Anyway, it is out there.
Other loads were developed from friends' recommendations or from specific manuals, but I have gone down in bullet weights and been very pleased with the results. I am shooting my Rossi replica M-1892 .45 Colt with two loads, both using 200 gr RNFP bullets.
My everyday load runs 1088 fps (at 10') with 6.3/TiteGroup/200 RNFP using CCI 300 LP primers, in WW brass seated with a firm crimp at 1.585" COAL, which also works nicely in my replica '73 Colt revolver.
My accuracy load is 10.1/VV-N330/200 RNFP using Winchester cases, crimped at 1.582", CCI 300s again. I got @ 1315 fps on the chrono with this one, plenty powerful, with one-hole grouping off the bench. I was bowled over at the accuracy potential of the .45 Colt using this recipe, YMMY.
Please work up to this last loading in your gun and be safe.