Some proposals to balance pass Engineers.
1. Access gates to be reviewed - why 50 kamitra cigars? That is saying we expect you to sit at a station and wait until you have collected the max allowance of rare you can get and then travel to me and then repeat that 4-5 times. A more Challenging scenario is that you must supply me with 4 types of rare, collect from stations at least 150ly from my base and return whilst a gamut of pirates who have "heard the rumours" chase you all the way here. Why 200 tonnes of gold, why not 5 tons of each rare metal collected from a specific station which again is a distance away and you are then hounded by pirates. The task is difficult and challenging but not bloody boring!
2. Eliminate special effects. These take calculable benefits and add in a range of side effects that really mean balancing has little or no chance. You selected large magazine, you get a large magazine, not a large magazine with corrosive shots. I would move these special effects to become specific modifications and maybe lock the higher tier grades behind 2 or 3 engineers or if they can't be graded then they do not belong in the game.
3. Limit maximum benefit of engineer mod to 25% This is what you can get with rechargeable synthesis, the benefit is that you get this buff permanently but after some more data and material collection than what the one shot in ship synthesis will bring. This I think is also key to balancing, as a 25% buff assists a pilot, but doesn't necessarily engage god mode. Coupled with no longer having special effects means FDev have the ability to be able to balance mods without finding out that whatever they do the Frankenstein collection that players are able to roll up will not break gameplay experience.
4. Have all benefits attract a drawback, the further you push power the higher you push heat, or the further you push DPS the further you push power draw. You shouldn't have to contend with twerps sitting at Engineers rolling 59 times to get the sweet roll of max good and minimum drawbacks. The penalties for having a great enhancement should always mean players should have to consider the impact of their decision. This makes balancing attempts pointless as you have to take into account these extremes. Change the extremes to manageable ranges and a majority of OP god play will dry up.
5. Shield boosters, have them only affect resistance and limit to x per ship (maybe dedicated shield slots) this way you have known max shield values and known max shield resistances that you can cater the DPS of known weapons against these, it should also mean you can say buff cannons base damage by a figure and know the outcome of change across all permutations of engineering.
6. This is more a behind the scenes point. Use the 'Big Data' you have on players ships and load outs - as it's all stored against the player and look for extremes in DPS, shield etc and then model against that. More importantly, look at the average engineered FDL, Anaconda etc and then review changes on these builds, copy the configs and get Q&A to blast each other with these builds pre and post proposed change.
7. Review consequence of actions by player, if they get all cosy with Felicity Fraser then they get locked out of Selene, or Palin or whatever, so the route to maxing out all items on a ship will never happen, so you don't have to try and cater for God mode ships built by twerps who live at engineer bases rolling for the next mod.
8. Never ever, ever return commodities that cannot be bought to engineer recipes/blueprints. Players have a chance from using in game data on best places to get technetium or datamined wake exceptions through diligence, hard work or grind. Having a random mission reward be a critical part of a modification is just poking your players in the eye for the fun of it. If they return they are purchasable at stations and cost the values shown currently, ie. not items only the uber rich players can afford.
9. Do a mini interim Beta with the above just let players see it's not all doom and gloom. Engineered ships can still be feared, but 45 min battles between them are a thing of the past as well as Eng vs non Eng encounters can be more survivable.
TL;DR hack and slash at its fundamentals and don't introduce extremes.