I can't help but wonder: Chakotay's ship was said to be about 40 years old and therefore outdated. Before being Chakotay's ship, the model had a different and indicatively smaller cockpit. Should we consider both to be the same craft?
I vote yes, because of the effect they tried to achieve with those two different cockpits. The original one indicated shuttle interiors and gave no hint of further spaces beyond the set; the one from "Caretaker" indicated that the entire redressed-runabout interior set was but a command center and held a fraction of the crew/passengers, and this set still occupied only a bit over half the volume of the original alien-shuttle set.
If Chakotay flew a
Ju'Day, then the smaller craft is obviously from the same manufacturer and probably named
Oku'Day.
As for the resources available to the Maquis, in DS9 "The Maquis" it was indicated that the organization had only two truly combatworthy ships - the two flown against the runabout fleet at the end of the second part, later identified as modern Starfleet fightercraft. Yet the Maquis had many ships in their possession even back then, including the torpedo-toting "auxiliary courier" that Sisko faced in part one.
I'd like to think that the Maquis had access to a number of large ships designed for noncombat tasks, and these included a large number of legitimately owned colonial
Ju'Days. Arming these to combat standards was slow work, though, so only the two purpose-built and no doubt illegitimately obtained warcraft were ready for combat at the time of "The Maquis II". The guns on the
Ju'Day ships would largely be retrofits, then.
I doubt the Maquis ever built any ships by themselves, as shipbuilding sounds like a major undertaking. Rather, they'd have converted existing small and medium vessels, which they probably had in staggering quantities thanks to the colonial lifestyle. After all, several episodes indicate that it would be no problem for a colony in the DMZ or other contested areas to provide a lift for a small band of Maquis, or sometimes even to evacuate the entire colony.
The converting could take an industrialized, standardized form, though. Thus, all of Eddington's
Ju'Days in "For the Uniform", plus Chakotay's ship in "Caretaker", would look identically different from the original, unseen civilian/lightly armed
Ju'Day. The ships do look heavily greebled over; perhaps the civilian/lightly armed form lacked the clamplike weapon things at wing roots, the various clusters of sensors or jammers or whatnot, and possibly even the wingtip cannon.
Timo Saloniemi