Coolant lines to intake and TB
 

My '91 is generally a track car and good weather car. I'm working on simplifying things under the hood while also installing MS and my Rotrex.

Can I remove / cap off the small coolant lines that run through the intake manifold and throttle body?

Never been done. Ever. Your TB will freeze immediately and the oil won't flow. Doubtful the car will start.

I'm afraid I will need pictures to make an assessment.

Great! It will work perfectly then.

On 1.8s the other end of that coolant line runs to the oil cooler/warmer, I'm assuming it's the same on 1.6s. Unless you've got a separate oil cooler you probably want to leave that section. You can just bypass the throttle body in/out on the throttle body and leave the rest.

the 1.6 doesn't have the oil cooler / warmer. I do have an oil cooler added in.

I was worried about idle valve function but I don't see how that will be an issue.

The wax pellet air valve will no longer work, or at least take much longer to close. The IACV will be unaffected.