An elderly neighbor of mine gave me an 06 Winchester (the short, round-barreled version of the 1890). I recently got it out and cleaned it up and tried to shoot it. Despite the fact that the barrel is labeled "Short, Long, and Long Rifle" it would not feed LR from the magazine. With just a little examination, I found that this was originally a short-only model, on which the barrel had been replaced. That isn't surprising, as black powder shorts probably rusted out barrels faster than any other round known to man. The opening in the magazine is shorter than a long rifle, although it is easy to get them into it. The main problem is that the recess in the lifter is too short to receive a LR round.
I took off the barrel and stock, clamped the lifter vertically in a small drill press vise, and clamped that vise in my big mill vise. This allowed me to get the lifter under the quill without removing the lifter from the action, which is not a simple thing to do on these rifles. I ran a quarter-inch end mill in to the length of a LR round. If I were doing this more than once, I would buy a 17/64 or 9/32 end mill. As it was, a quarter was what I had, so I had to open that part up a little with a Dremel and a dental burr. I now have an 06 with a good bore, that is fully functional with long rifles.