Since I don't have the ejector rod installed on any of my three conversions either, (2 of which have shortened barrels, and the one with the original length barrel has a non-ported backplate) I can't say how they would work or not. (Although Will is correct, the loading lever is supposed to be notched for the ejection rod, and the rod wouldn't disengage unless the loading lever dropped during firing....which it's not supposed to do.)
Although I think if I was going to go that route, I would probably buy and install a Colt Peacemaker ejector rod and housing instead. In other words, remove the original Remington loading lever, install the cylinder pin retaining clip/spring, and braze on the new Peacemaker ejector rod housing.
Once you port the frame there's legally no going back to percussion anyways
By the way, I had trouble with recoil disengaging one of my .45 ACP cylinder pin retaing clips (the 'stock' replacement retaining clip engages the cylinder pin only about 1/8"), so I made a new one out of damascus steel that engages the cylinder pin a good 1/4". I'll have to take and post a picture of it...as the damascus pin against the nickel frame definitely looks 1800's