Now this is just bonkers o_O
Okay, uh, where do I start...
Most of the changes you want to do are better off doing with Minetweaker. Definely do not remove dust smelting, that's ridiculous, it makes the Thermal Centrifuge and Tiny Dusts useless. You can disable macerating ingots into dusts, but if that causes exploits, then something is seriously wrong. The Blast Furnace doesn't require Iron Dust, it can use any form of Iron, even the raw ore.And DO NOT Edit the jar, you can't even do that with the api, there are better and easier(and also ALLOWED) ways to change the recipes.
Thanks alot for such a quick response, I'm a bit of a novice at this stuff. That theory was cobbled together after a few hours of searching round the net.