I got some e-mail from someone who says that he is a retires Colt Armourer. He had an interesting tale, that if true, explains everything.
The best info I've gotten yet was e-mail from a gentleman whe says he is a retired Colt Armourer. He says that the frame was most likely a New Service made in 1903 based on the serial number. He said it was not unusual to have frames sitting around on shelves for years. I guess they just pulled from the front of the shelf and so some older ones might just sit back there.
He said the barrel looked like the ones for the "Improved New Service" that came out in 1905. That was also the year that the 45acp Cartridge was first introduced. It was designed by John Browning and based on a modified 38 super.
There were, according to him, some revolvers chambered for the cartridge as well as what later became the 1911. Both were submitted to the Army for evaluation beginning in 1906. He thought that this might well be one of those early test guns which would account for it not having any model designation on the butt of the frame, for the non-standard barrel and sights, for the trigger and extractor work and for the modified, but not presentation quality, grips.
Anyway, true or not it's an interesting story and a mystery that's unlikely to ever be solved. Sure does shoot sweet though.