With this mod there is no way to craft warponium fuel, because the nuclear fuel recipe is removed by IR3.
There is no rocket fuel anymore, and rockets use liquid H2+O2 instead of rocket fuel.
There are 2 problems here:
1. Warp fuel can't be crafted, and there are 2 late game recipes dependent on warp fuel. The affected recipes are warp nuke and warp port.
2. Even if there is a way to obtain the fuel, they can't be used as vehicle fuel. I'm pretty sure it's designed to be the highest tier vehicle fuel in original warptorio2. IR3 changes all vehicles to use batteries and canister fuel, and no longer use solid burnable fuel.
This is actually more of a design flaw rather than a bug.
My suggestions:
1. Change the nuclear fuel in recipe to something obtainable in this mod. I suggest empty high pressure canister. The warponium fuel cell is enough for the feel of 'some warp magic in the fuel'.
2. Change its fuel type to canister fuel or charged battery. I prefer charged battery, because IR3 adds a vehicle that can only use battery and not fuel canister.