The CTO prevents vacuum from passing through the valve when the engine is cold, to prevent the EGR from operating and the emissions canister from purging. If the CTO were stuck open, I would expect the idle problem to also occur when the engine is cold, the EGR would operate too (which it shouldn't when cold). If the CTO were stuck closed, then the EGR and canister wouldn't function at all hot or cold. From what you described, it makes me suspect a problem with the canister. Some sort of vacuum leak with the purge signal line.
If you're looking for a new canister, just swap in a vacuum canister for a '90's 4.0L Wrangler/Cherokee. This canister will have the tank vent line, purge line, and purge signal line you need for the Howell conversion and won't require capping any ports. I put one in my YJ when my OEM canister went bad. Seemed to be a bit more snug of a fit than the OEM, but no problems otherwise.
FWIW, for any other folks that come across this post, the 4.0L canister can also be modified to work with carbed YJ's by drilling open the plugged port to hook up the carb vent line.
The OEM part number for the 4.0L canister should be 53030500. I got mine from rockauto.com