Well, I really like a number of your hullmods and they've become essential to my campaign play over time, PD Pep and the Cargo Carver and Cargo Pods mods in particular.
I did my best to balance them but also make them useful and it is good to hear that they have been a help. Your post made my day, truly.
The only one I thought might be a little underpriced was Fetch Deck for pure carriers, but that's mainly because post-nerf Expanded Deck crews is so bad I never even consider taking it anymore, and Fetch Deck used to be exclusive to JYD hulls as a little bonus for them.
When you say underpriced, do you mean credit cost or OP cost? I really had to think whether or not to keep that as JYD only but eventually decided to open it up to all and let it be free 
Thanks for all the work you've done on both JYD and this new collection, and for being clear about the transition.
I really struggled whether or not to make this move but at the end of the day, the point of my mods is to give players options. Having all those built in mods on JYD ships took agency away and forced players to use them if they wanted to fly a JYD ship. I'll keep at it and if you have any suggestions or ideas, you have my ear.
Okay, got a few suggestions 8-) I meant OP cost for Fetch Deck, but after testing for a bit I have come to the conclusion that it is fine (it is a 10% decrease in the rate of decrease of replacement rate when the wings are understrength, the same stat that Expanded Deck Crews affects, rather than a flat 10% bonus to replacement time, which is what I thought based on the description). The problem is Expanded Deck Crews just isn't that good for the price anymore, not that Fetch Deck is overpowered.
Okay some balance stuff. My goal with these is "keep them cool, but make penalties noticeable": Do not decrese the bonus or increase the OP cost, but make it affect things. None of these would stop me personally liking and using the hullmods where appropriate 8-)
PD Pep: Cost the same, effect the same, double the CR decay penalty from 5% to 10%, and possibly add a 5% flux cost increase for PD weapons if that is not too much of a pain to script. For most PD weapons, that isn't very noticeable, because they tend to be low flux, so it will mainly effect long range dual use PD_ALSO weapons, like the Devastator, and the "everything small is now a PD weapon, whoa they got 50% more range too" effect that IPDAI has with PD Pep. And those are exactly the two cases where you want a noticeable drawback because they are rather powerful. Yeah, you get the range but you have to pay a bit more flux for it. Seems fair.
Cargo Carver and Cargo Pods: Decrease the Max CR of the ship by 5% for both in addition to current penalties. I toyed with the idea of imposing a supply cost to add or remove the hullmods, and this does that among other things - and neither mod is something that you want to be happy about on a ship that is getting into battles, and will give a small penality for mining.
Rationale: Cargo carver - you aren't actually chopping out hull, you are just stashing cargo in places that will interfere with smooth operation of the ship by the crew and damage control - hence lower CR and less hull.
Cargo pods - great big pods hanging off the ship - harder for it to efficiently manage as well as making it a slow fuel hog 8-)
The code for decreasing max CR (from the vanilla Increased Maintenance D-mod, using applyEffectsBeforeShipCreation) is this:
"public static float MAX_CR_PENALTY = 0.05f;
...
stats.getMaxCombatReadiness().modifyFlat(id, -Math.round(MAX_CR_PENALTY * effect * 100f) * 0.01f, "Increased Maintenance");"
Others as I test more, but those are the ones I use most. I think Brawler Missiles could stand to have the cost lowered, because I can't see using it on anything except an SO ship since the range on Pilums and the Drill LRM got lowered - but I don't tend to run missile spam ships so I will defer to the experts there. I guess it could be useful on a ship using exclusively the Kadur Jericho and Jaya missiles (those are range 6k and 10k and not very manuverable) but in both cases you probably want ECCM first so its getting to be a lot of OP. And Brawlers utterly trashes range and preferred engagement range for most small missiles, so it has a big penalty already.
More as I test. Hope this helps.
