Does anyone use both of these mods? Are there any recommendations as to which I should load last? I suspect the TR Census and Excise Travel Links to be loaded last. Or are they just too incompatible?

IIRC I used to use them together with no problems. I think TR Census and Excise Travel Links doesn't enable its ship and stuff until after Chargen, so they should be fully compatible. And if they're not compatible for some reason, you'll find out within a couple minutes of starting the game, so it won't really hurt to try.

They're compatible.