I also have a very nice Marlin .41 mag (M94S) that I got on gunbroker 7 or eight years ago now. After checking it out when I first got it, and satisfied it was ready to shoot, I loaded up some store bought, pre-lubed, 215 grn. semi-WCs, which were sized @ .412 (maybe .411s may have been better) and took it out to the range.
After shooting it a half dozen times I realized from the 6-8" pattern I was getting from 50 yards off the bench, I knew I had an issue. My thought was, "Yeah, that's why it was offered on gunbroker..."
After doing the lever and breechblock disassembly (really love the Marlin design and easy takedown to clean from the breech), I went to cleaning. After a fair solvent, patch and jag session, I looked down the bore and could see a bunch of little dark pock marks in there. I knew exactly what those were from past experiences shooting my Sharps rifles (B.P. and cast bullets). So, I went to my next step...
I have some bore solvent made by a company called Shiloh Creek, and their lead removal solvent is first rate. Problem is, it's near impossible to find anymore. I've heard it's still available, but I've yet to find any more on the market (luckily, I have a fair stash of the stuff, and I rue the day when I run out). BUT, there's another outfit that offers a lead removing solvent and they claim it's every bit as good as the Shiloh Creek stuff. Here's the website:
www.sagebrushproducts.com
When you get in there, go to the cleaning supplies box and click on it. Then click on cleaners and lubes: then find the "Extreme lead remover" offering. It's supposed to be very good for the problem.
Also, how aggressive are you getting with your solvents and jag? I know when I have a bad leading issue, I use a very, very tight, solvent filled patch on a proper jag and tap (lightly; just enough to keep the rod moving) the rod through the bore with a rubber mallet (use a bore guide, too). When I did this on my .41 after that first shooting session, I was getting shards of lead over 1/4" long on the patches, and it took quite a while using this method before I didn't see any more lead coming out on the patches (I use 100% cotton patches, too). I can't help but think whoever owned the rifle before me either didn't know about leading problems, or thought the gun was just plain inaccurate (just speculation here, certain sure).
Also, when shooting cast bullets through any of my rifles, I don't use a brush at all; just solvent patch and jag until I don't see any more lead on the patch. Then, I put a couple of dry patches through the barrel to get the excess bore solvent out, followed by a lightly dampened patch of gun oil.
After that lead-borne cleaning session, I loaded up some Speer, Deep Curl, H.P. jackets and took it to the range again. My first 5 shots off the bench at 50 yards gave me a group of just a tad over 1" using just the factory barrel sights. I've been using those bullets ever since, and have since had that same accuracy using a 20 grain charge of H110 under those Speer bullets. I also have no doubt that the rifle will shoot even better than that if I just had my young eyes again. Still, I'm happy with the accuracy with my old eyesight.
Some will say the micro-groove barrels aren't good for shooting cast, and others will say that's not true (my JM, .41 has micro-groove). At this point I can't say one way or the other. I just know I had some bad leading in my .41, and you may want to try my lead removal method or not. I know it works for me.
On shooting my Sharps rifles (I have two Shilohs; 45/70 and 45/90), and using B.P. and cast bullets (no gas checks, either) my leading issues come from when I shoot a fair amount on a given day (say 50 or 60 rounds) and the weather's quite warm; that's when I'll have an issue come the end of the day when the cleaning begins. I'll usually pull some lead out of my 45/90, but it's never terribly bad, and my accuracy is still there even after that last shot.
Hope some of this might be of help. Good luck "getting the lead out."