First of all - thank you for your work.
If the author does not mind a little criticism, I will allow myself to say a few words.
The mod is quite structurally good and theoretically meets all high quality standards.
For example, that ship changes now spawn and can be looted is a good idea, as is the scanning system.
The problem is exclusively in the field of changes in the characteristics of the ship itself. The penalties imposed by the changed state of the systems force the player to refuse to apply the changes. The player is PUNISHED for bonuses. And while the bonuses are negligible - for a lot of money.
I understand perfectly. that the respected author tried in the so-called "balance", the meaning of which, from my probably erroneous point of view, is exaggerated by the author - probably as a result of the horror he experienced from flying monsters that could be created in the previous mod.
I would take the liberty of suggesting, to the respected author, that the penalties increase exponentially as the number of bonuses increases - completely abandon them in the first three levels of improvements.