First of all I would like to congratulate you on deciding to shoot this wonderful antique in its original caliber. It is only a bit more difficult than most but the rewards are very worthwhile.
The first thing you will want to do is slug the bore of course if you haven't already done so.
I use a Lee #14 shell holder on my modified 44-40 brass. I use a modified Lee case length tool in my drill press to make these. I have also purchased some from Fig33 and I can recommend him with confidence.
You can also use 44 spl (or magnum) brass. I think the 44-40 is better to use as it fits a bit better but it is a little more work than the 44 spl.
I have 2 different bullets that I shoot. One is 165grn LRN and the other is 215grn LRN. These are cast from a mould I purchased from Bernie at Old West Bullet Molds. Both of these bullets are of the heeled type. I also purchased a crimping tool from Bernie and I recommend it as well.
I use 2.5grn of Trail Boss in mine but yours may be different with a different bullet depth / type etc.
I prefer to use FFF black powder as this recreates the original cartridge and therefore the original experience. Black powder is a wonderful thing with the flash, the smoke and the smell. A very tactile experience. Not sure how many grains of black powder but it is a filled case, barely compressed when the bullet is seated.
Trail Boss is a very unique powder in that you can figure out a good load based on the volume of the case. More information here:
http://www.imrpowder.com/PDF/Trail-Boss-data.pdf
Also there is a handy chart for shellholders here:
http://www.handloads.com/misc/shellholders.asp