[PvK]

No, you're on track. It depends on what you change and how you change it.

AI research is handled in each AI's research file, which is a straightforward script, with sections for which situation the AI is in (so it can research Stellar Manipulation when it gets cut off).

For 3 more levels of Shipyards, you could simply go find the point where an AI researches to SY level 3, and then either change that to 6, or go add appropriate places for it to research 4, 5, and 6, via cut & paste.

If you play with components, you may need mod ship design, etc.

Note that each specific AI has its own set of files, but there are also default files for races which don't have all specific AI files.

PvK