Whole thread is too long for me to read right now, so maybe this has already come up, but here are my .02 credits:
If you want to be compatible with and able to use the vast wealth of standard ships and ships designed by other people, you don't mess around with the various drive parts, tonnages, and fuel usage. Instead, you just re-define how these parts function in your TU.
If you want a one-day jaunt drive, there is no need to change anything in the design process, just re-define a "jump" as working the way that you want it.
In fact, as long as the tonnage works out the same, say you don't want that much fuel usage, just re-define part of that as being some other component of machinery. The key is to have tonnage of required stuff work out the same, so that you can use standard designs.
Oh, and if your jump/jaunt/hyper/warp/whatever doesn't have anything equivalent to J-1, J-2, J-3, etc, then just re-define those as well. Maybe drives sized for J-1 give one distance, or speed or whatever, whereas J-2 sized drives give slightly improved performance in some way, J-3 slightly better than that, etc.