as far as running goes you might want to think about getting a head gasket kit. and pulling it. have it pressure checked. put new stem seals on the valves and jet valves and replace o rings.
hopefully your head is not cracked check your timing chain set up and silent shafts flush your radiator.
find a stock manifold and invest in a webber carb if you have a bad carb. of course its a debate over stock or after market
for carb i like the stock ones when they work right. but to many things to go wrong and the price of them u might as well go after market. i prefer the stock manifold over header. i didnt notice any difference in power just noise and heat. theres a lot of knowledge on this forum and all you have to do is ask. the 2.6 is a love hate motor. haha
there good if you take care of them. rebuild them right. and dont haft arse them. iam getting ready to rebuild another one and iam keeping the balance shafts. i dont like the feel
with out them they get buzzy in 3-4000 rpm range.