Welcome to the world of Civil War arms. First, the experts are the North South Skirmishers Association.
www.n-ssa.org This website is frequented by skirmishers, sutlers (merchants) and gunsmiths who deal with these weapons. Were it not for these gentlemen and women, these guns would be a lost art. There is no aspect of these supposedly primitive weapons that they cannot advise.
It is not surprising that your Enfield shoots high. These guns were intended to shoot 500 yards and did so with great effect. DO NOT modify your rear sight. Enfield rear sights are wonderful as is. Your problem is that the front sight is too low. To shoot 50 & 100 yards, you need to install a new front sight, higher than the original. The new front sight should be dovetailed and brazed to the barrel, not welded. There are gunsmiths who deal with these guns on the N-SSA website. Once you KNOW your load, begin sighting at 50 and 100 yards, shooting to point of aim. Slowly, carefully over several sessions, file down the front sight, carefully checking the point of impact. The Enfield rear sight has 2 short range positions, with the sight sliding front and rear. To set the sight to 50 yards, set the sight to its rear and lowest position at rear. To set the sight to 100 yards, slide the rear sight to the hump at the front end. The drop of these rifles is pretty incredible. Shooting 200 yards and beyond requires use of the ladder type sight. Again, DO NOT modify the rear sight in any way. It is excellent as is.
Your gun probably has a 0.577 or 0.578 bore and is intended to shoot a Minnie. The problem is what diameter? The bullet needs to be 0.001" less than bore diameter and that may take some experimentation. First check bore diameter with calipers. A Lyman 575213 mold is a good starting place. You will need to size the bullets and you wont find appropriate sizers on any reloading manufacturers website. North East Trading Co. makes a great little sizer that fits into a RCBS Rockchucker. Bore sizes for Civil War muskets run from 0.575" to 0.578" for the Enfield and 0.578" to 0.580" for Springfields. You may need to try different sizers to get the right one. These guns can be incredibly accurate with the right bullet diameter. You may need to try a couple different molds before you find what works for you. Use pure lead bullets only.
The best way to learn the manual of arms for these guns is to attend a skirmish or a practice shoot by N-SSA members. The advice they can provide is literally invaluable. If you go to the N-SSA website they can put you in touch with a team and you will very likely get an invite.
These guns are intended for black powder. Forget substitutes like Pyrodex, which has a real serious tendency to hangfire in large diameter bores such as 54 or 58. DO NOT hot rod these guns with loads similar to a Hawken. The usual military charge was 60 grains of FFG black powder.