Since you said that the .36 was shorter than the .44 I am going to guess you are looking at Remington models. The .36 remington that Pietta makes and Cabelas sells isn't an accurate representation of the Remington Police, if that matters to you. It is the same frame and barrel blank and cylinder blank as the .44 just drilled different. The lead will run basically the same cost for .380 balls (which you should use) and the .454 (ditto). Caps the same; felt, if you choose, the same. But it will eat less powder. I know someone on here has a .36 with target sights. I don't know where he got it, but it is sweet looking. The .44 is availabe with target sights from most retailers
For converting to cartridge, everyone else has said .44 and I agree. Better bullet fit and .45 long colts are easy to get and easy to reload. The new cylinders will basically cost the same for either caliber.
If I was buying my first gun now, knowing what I know now, it would still be an 1858 Remington with a second BP cylinder, but I would spring for the stainless steel. The extra hundrend bucks is worth it for peace of mind and ease in cleaning. Of course, I now know that I want to shoot the damn thing all day long, every day.