Highlander, I also have a EMF 45-0 with the 28 inch barrel, double set triggers and standard grip on the stock.
This gun will shoot a lot better than I can even though it is truely the poor mans version of a Sharps (Not trying to rain on your parade, I found this out after I bought mine.) I agree, have your barrel slugged to see what type of diameter slug to shoot.
There are a lot of 45 cal diameters out there, everything from .452 to .459 and I have even heard of larger. Of course there are also a large varriation of weights for each diameter slub also. I have a digital set of calipers and you can mesure at the crown and get the different lands and groves measurements there. Another way to slug the barrel is to take a soft lead round ball that will just set on the chamber end (say a 50 cal ball) and gently start tapping it through the barrel with a wooden dowel. I recommend the dowl be short at first until you get the slug started down the barrel about 6 or 8 inches. Graduate up to a dowel that is as least as long as your barrel and continue tapping the ball through (use a soft mallet of some kind)
It sounds sort of intimidating to think about pounding a slug of lead through the barrel but it will work. If you are squimish about it and have a gunsmith close by you can have them do it. Or if you have no other alternative send the gun in to emf and requestthey do it. Anyway, once you have a chunk of lead driven through the barrel, it is now time to meaure the slug lands and groves with a good set of Calipers (Midway is running a special this Month on a good set of Didgital Calipers for like 20 bucks pluss shipping) The diminsions on the slug will tell you what you want to know. Most 45-70 riffles are going to take a slug between the .457 to .459 according to what I have read.
Another possiblity causing accuracyproblems could be the chamber depth. Measure your rounds buy putting a non loaded, non primered shell in the chamber should be just finger crimped. The slug should be slightly extended past where the crimp groves are. Push the shell in the chamber until it meets resistance. Continue to push it in untill the action will close normaly. Carefully remove the round and measure its OAL (overal length) This will let you know how deep your bullets should now be seated at the reloading bench. This can also be done by any competent gun smith and recorded for you but If you are able to relaod your own shells this should be no biggie. If the bullet is forced to travel any distance at all in the non riffled portion of the chamber to get to the riffling you are loosing accuracy.
You did not say if you are hand loading, what type of load you are using and what type of powder and primer you are using. Are you shooting from a supported bence or Off hand.
I recommend you bench test at 25 yards and build a data base from there.
Best of luck and Vaya Con Dios.