I'd suggest doing some simple checks to make sure the internals are good. First that comes to mind is a compression check. I'm making the assumption that you keep up on maintenance, plugs, wires, cap, rotor, oil, filter, fluids from axles up, ect?
On my original 1.3L I had a exhaust header and oversized/less restrictive air filter (don't know who made the filter) on my 87 Samurai. Drive line was stock. 3.5 S/R lift. On original sized tires I can run down I-70 around 80 mph. Don't get me wrong it takes a bit to get there but maintains real good. When I stepped up to 30" tires that was a different story.
I agree with Drone637. Your best bang will be breathing. Air in, Air out.
I am in the process of swapping engines. Going to a 1.6L 16v.