You'll find many of the values in the higher scales to be off and require homebrew solutions. I recommend taking a look at the 3057R TRO for the mass details of shipyards and the limitations of pressurized and unpressurized yards. You could speed up the construction of a warship with a large pressurized yard, but you'll be limited to building vessels smaller than 500,000 tons, which the Bonaventure falls under at 240,000 tons.
To keep things as simple as possible I would use the Base Construction Tables found in the Campaign Operations rule book under Force Operations}Additional Rules}House and Base Building. Apply every Structural Modifier you see with the exception of Environmental Sealing if it is an unpressurized Large construction yard. You would obviously have to apply this to the Yard's construction itself, unless you are reserving the use of an existing 1st Succession Wars yard (off the top of my head I can't say in what source book these would be located). Apply the Fortress values for days per hex/level. Set bays as hangers with the height as levels (2 for mech). Assume a trained crew.
On a side note, you should know that most of the warships you are playing with are already existing and have no need for building or constructing any of them. As grand of an idea of building a warship is, there was very little time spent on just how to get along on doing it and I suspect the ludicrous time frame given was an easy way out of providing clarification or rules specifically for this. Either way, you have MANY warships to play with that are pre-generated and the entire idea can go on the back burner for a future campaign. You don't need to build anything in the Succession Wars campaigns. These warships are handed to you from the start.
My kudos for your confidence on starting the ISaW campaign. I myself am still daunted by the prospect and magnitude of it. That and the actual need of players in my local area obsessed enough by the scope and idea of such a campaign to stick with it. Most people are intimidated enough by the Core rules. ISaW is highly deceptive as most people never realize how much information is carried over into the larger scales. Things break. Rules become vague and insufficient:
To construct the 42,000 ton Large unpressurized Yard would take an unmodified 420 days x 10.15 (borrowing the figure of 'capital armor at 100 tons/day' x all modifiers). That's almost 12 years. 5 years in a pressurized yard that would remove the x5 modifier. Yeah, wrap your head around that one! That's not including the bays and other equipment. At least this is how I would do it, but the results are as ludicrous as the estimate that caused the original complaint. A warship is ten times the mass of the yard. The only way around this would be to build multiple yards that would stretch across the entire hull of the warship and have them all build with some kind of cohesion by working on separate parts and thereby decrease the production time for a single warship. The same can be done for the yard. I have no idea how the Crew modifiers would work in micro gravity to reduce the total construction time. Neither do I know how many hexes or levels per day would apply to warships. The closest thing I can see for a conversion is the "300 tons per hex for every 4 levels of structural height" for open hanger construction (just to pull something out of the air) in AUE's Adv. Support Vehicle Construction section under Construction Factor and Internal Weight Capacity. Though this limit was intended for internal weight capacity for equipment. Anyway, that would be 140 'hexes' and days for the hanger if it falls under a Light construction multiplier of x1, 800 hexes x 11days (medium Fortress) = 24 years for the Bonaventure.
In the end, it is an impossible feat, since no one would allow this to continue unprovoked, or it would be completely ignored as the cost and exaggerated construction times become a tactical benefit to your enemy. It could never be kept secret with so many crew working on the yards. You only manage to repeat the source book material in making the construction yards the first priority target in any war, followed by the ships themselves, which just get murdered under the higher scale conversions that skew armor against a much higher damage potential. Everything melts and disappears in warship confrontations so quickly it is ... anti-climactic.
FYI, you'll have to make your own list of Warships and jumpships. These are not provided in the source books as far as I remember. You're just getting the plain flat number of how many warships were available to each faction/house. The jumpships will come with the Combat Commands if you assign them at their creation. These remain generic and unseen, having enough docking collars is, I think, assumed.
In my opinion, just roll for the ship on the custom RAT's, keeping these as generic as you can and have just 4 types: Corvette, Destroyer, Frigate, Cruiser, with a 2d6 roll for them 2-4 (least favorite); 5-7 (3rd best); 8-10 (2nd best); 11-12 (biggest).
That's about the best I can give atm. I'm still working out tidbits here and there as I return to the idea myself. Good luck, my ambitious friend.