Experimenting on my own I've found the navpoints get a little screwy (on my build) when the player is not the wing leader. Doesn't appear to be Woolie's fault.
Woolie, I really do like the MOD. I feel like I have some firepower, but the fighters are still able to avoid fire so I don't feel like a sitting duck. It's quite nice to have to avoid Anubis autocannon fire to destroy bombers, or go after the Anubis while the bombers rip apart your convoy (I've played with it in FRED). I have some criticisms, but please take them as friendly from somebody who likes the way it's going.

The GTVA didn't produce beams until 2355 (I believe). How would the Terrans, without the Vasudan's help and without any Shivan technology (and without the Shivan 'threat' of coming back to scare them) to study make them 15 years earlier? I think flak cannons could come around (not the same as GTVA flak...but any kind would mess you up) at around this time though.
Shields? The MX-50 tech entry mentions the famed Ross 128 Deflector Array, however I don't think shields would be nearly as strong as they were without Shivan tech. I'm sure they had been doing research, but the main Freespace campaign gives the impression the Shivan tech (and Vasudan help/scientists) was a real advance. Also, I love the balance of fighting without shields. It makes things harder, and missions have to be designed slightly differently to take this into account (players also have to fly differently. Stay away from warships). I'd hate for the player to gain access to shields within the first few missions and throw all that opportunity of something different out the window. Perhaps weak shields, or shields that don't recharge over a mission?
I like how it's based on the freespace port, it makes it more authentic. A lot of the reconstruction era ships I think you should leave out. At the time of Freespace 2 the Charybdis is new, if not brand new. You might consider replacing the Terran gas miner with the Bromios from the TVWP (it would at least add a bit of continuity to the two campaigns). And maybe even add in the Reliant, a destroyer that's been in service since the Unification War (I'm almost positive it was released with the demo...).
Now to stuff I liked:
Although not canon, I do like the railguns. They add a lot to capital ship battles.
The nav point and autopilot system is great. It really lets me feel like I'm "based" off the destroyer.
I like the Phalanx. I've tried to make weapons intended for this era, and it's hard. If you make them much more powerful than the ML-16 Laser they're overkill, if you make them weaker they'll never get used. I liked the autocannons (Terran and Vasudan). When you arm an Anubis with them, they can actually hurt you. Kudos for making them fairly balanced.
I liked the Cobra and Vasudan Autocannon trail. It just looks awesome...
If you need anybody to test or help out with stuff, let me know. I don't have 24/7 free time or anything, but I'm experienced enough to take on what I can chew (unlike 13 year old me 6 years ago trying to start and run the TVWP...glad Goober took over, it's actually gone somewhere lol).