Howdy
It is always difficult to pin down information about Merwin Hulberts because they changed things from time to time, and all the factory records burned up in a fire. The most authoritative book on the subject is Art Phelps' book The Story of Merwin Hulbert & Co. Firearms, but frankly I find his writing to be so biased that it is sometimes difficult to separate fact from myth.
As far as I know, 44 caliber Merwin Hulberts were chambered for three cartridges; 44 Russian, 44-40 (44 WCF), and 44 Merwin Hulbert. The 44 Merwin Hulbert cartridge is an obsolete cartridge and it has not been manufactured for many years.
So the first question I have for you is, what are the headstamps, if any, on the cartridges you have?
The next question is are there any caliber markings on the gun?
Generally speaking Merwin Hulberts chambered for 44-40 were marked CALIBER WINCHESTER 1873 on the left side of the frame. This is because 44-40 was the most popular chambering of the Winchester Model 1873 rifle at the time. The two Merwins I have that are chambered for 44-40 have cylinders right about 1.560 long. It seems you have already determined your cylinders are too short for 44-40 cartridges.
The one MH I have chambered for 44 Russian is marked RUSSIAN MODEL on the left side of the frame.
This one has a cylinder right about 1.480 long.
Sorry the markings are a bit indistinct, it is an old gun and it has been refinished.
I do not own a MH chambered for the Merwin Hulbert cartridge, nor do I have a 44 MH cartridge in my collection. If your MH has no cartridge markings on it, perhaps it is chambered for the 44 Merwin Hulbert cartridge. I really do not know.
This is the only photo I have been able to come up with of a 44 Merwin Hulbert cartridge. It was made by the Union Metallic Cartridge Company. The head stamp is U.M.C. 44 MH&Co. I believe this cartridge is a bit longer than a 44 Russian, and not as long as a 44-40.
I also cannot help you too much with cartridge dimensions. The best I can do is give you some information from Phelps' book. Caliber was actually .42. (.416, .420, .421). Rims varied in diameter; .489, .499, .500. Some rims had a pronounced bevel. Case head dimensions varied too, .437, .438, .440. Overall Length; 1.525, 1.512, 1.526. Case Length; 1.140, 1.157, 1.159. Phelps notes say the cartridge appeared to be a slightly undersized 44 Colt.
In addition, a reprint of the 1887 catalog states that the 44 Merwin Hulbert cartridge held a powder charge of 30 grains of Black Powder.
Lastly, my friend Happy Trails used to use 41 Magnum brass, of all things, to make up cartridges for his Merwin Hulbert chambered for the 44 Merwin Hulbert Cartridge. I believe he trimmed the brass down, but I do not know how much. He may have been putting a bevel on them too.