Okay, so here are the results:
- the stuff with Science 18 was indeed a bug: my code did not ignore disabled technologies, so it thought that Stack Inserters were a technology without a prerequisite, and connected Science 18 there.
- for such an overhaul mod, Industrial Revolution does not delete a lot of vanilla items, apparently; the only in-game problem (as far as I can see) is with the Steel Furnace (IR2 does not reuse it for some reason, as it does with other objects).
I replaced some of the items in science pack recipes with others; did not balance the costs, so if you feel that some science pack costs too much or too little, please inform me of that.
The changes are in the 1.0.4 version.