Converting the Jumbo, hmm? It's got the room, certainly. Sticking in the second engine, however, well, I think that'd mess with the structural integrity, myself. The ship clearly wasn't designed with that sort of thing in mind. But such is a fluff issue, and one commonly ignored in such significant modifications, because it (strangely) isn't an issue for BattleMechs, where an engine takes up the same internal volume regardless of whether it's a 120-rated engine making a 40-tonner go 3/5 or a 240-rated in that same 40-tonner with twice for twice the speed.
Otherwise...you didn't include gunners in your crew breakdown, but it comes out to five. Assuming you don't want to add more officers, that makes 4 officers, 19 crew, 5 gunners. You're working a far more complex ship with only 60% of the crew from the civilian version; given that clunky systems were said to be why the Jumbo needed a large crew to begin with, I think it makes a better "feel" if you have to increase the ship's crew much better. Little known fact, but merchant sailors are traditionally more highly skilled than naval personnel, at least at the tasks actually related to making ships move about. But naval vessels are far more complex and require much more maintenance, and thus the much, much larger crews despite the much, much smaller ships. To crew the Phoenix at about the same level as the Jumbo, I estimate you'd need about 9 officers, 40 crew, and 5 gunners, costing another 197 tons, but since you had 2786.5 to play with, there's plenty to steal from.
I'd also consider throwing in some small craft bays. 6-8. Possibly also some Marines, so the Phoenix can assist in customs duties during peacetime and help suppress piracy at all times. 30 Marines would cost another 210 tons, and 6 small craft bays would eat another 1200, but there's still 1239.5 left. Nice thing about small craft, they also give you an excuse not to increase the escape pod/life boat numbers. Throw out another 65 tons for food & water, 148 for 1% spare parts, and there's 1026.5 remaining.
Does the Phoenix need more than two years worth of fuel at 1 gravity, when the Concordat has enough fuel for 63 days? Probably not. Still, five times as much fuel, to allow for a more active DropShip and account for fueling the fighters, seems fine, which would cut the fuel to about 600 tons, pushing another 816 tons to cargo, for 1842.5 tons total (2055.5 if you don't divide out the food & water or spare parts). Which is pretty impressive for a dropship carrying so many fighters. Though if I were a Phoenix captain, I'd be using the DropShip's speed to stay away from enemy assault droppers & the full range of heavy fighters.