Osage,
What is "way more gap" than on your other Colts? How may thou, or how many strips of printer paper?
As to how to check whether you are bottomed out with the arbor, try loosing the barrel assembly from the locating pins and rotate it to clear the mating surfaces. Some are too tight to push the barrel onto the arbor when you twist them. You CAN drift it on with a rubber or rawhide mallet, then, if it is tight and will not turn, just use a straight edge to see if it passes the mating faces. If it will turn, you can juse twist it to see if there is interference of the surfaces.
If you have excessive cylinder gap, I can't tell you what you should do. It is your pistol. If I were to trim my own, I would take the excess from the barrel surface, rather than the frame surface.
Went back to read your OP and it seems to me that you have no problem with the hammer not going forward enough to fire the caps, to overcome any cylinder gap. It seems to me more like the caps are being seated at the first snap of the hammer, then, fully seated, fire on the next snap. Sounds like fat cones, to me.
I hesitate to suggest you try hammer seating of the caps. Hold the pistol downrange and press the hammer firmly. It "should not" fire, but it might.
If you feel any "give" when you do that, I would say the nipples are fat. Like trying to push 10s onto 11 nipples. Very hard to do. That copper cup is tougher than you might think. And, too, if it is too small, and you do force it, it forces open that "pleat"of the cup, widens it, the cap will probably not grip as well as it should, making a chainfire possible, though I think they are far more rare than many here think they are.
Check the gap, check the nipple diameter, use your other Colts for comparison. I am not going to go check my various nipple diameters to see what they are, but I will, later. That should be interesting.
BTW, Osage, are you too busy, or are you still making the loading stands? If you are still making them, let me know, and if so, e-mail me pics to pick the one I want. If you have quit this, never mind.
Cheers,
George