Not quite sure I follow. All I'm really interested in modding right now is the engines of my Courier.
First off, you do have the Enhanced Performance Thrusters, yes? If not then you can buy them from the outfitting section of the engineer's base.
As for the upgrades: there are multiple grades of modification, from 1 through to a maximum of 5 (although not all engineers reach this level). The modification for each grade is better than the last. If you look at dirty drive tuning then a grade 1 modification is minimal, grade 2 a bit better and grade 3 fairly decent (within the bounds of the RNG). You need two Specialised Legacy Firmware for grade 1 and grade 2 dirty drive tuning, but only one Specialised Legacy Firmware for grade 3. So blowing two of them on the grade 1 mod is, relatively speaking, rather wasteful.
Instead you could build up your reputation with the relevant engineer by asking them to carry out other modifications. 3 on-grade modifications will get your reputation with them up to the next level, so 3 grade 1 modifications will get you to grade 2, then 3 grade 2 modifications will get you to grade 3. These modifications can be anything that the engineer provides, so you could burn through some of your common materials to get your reputation with the engineer up to grade 3 and then get them to do a grade 3 dirty drive tuning. This will give you a better result thrusters-wise and you'll only need to hunt down one Specialised Legacy Firmware rather than two.