Not having the OEM computer setup simplifies things greatly. No sensors, no computer to mess things up.
As far as cat problems go, a plugged up cat would cause bogging under WOT - like the engine is hitting a wall it just can't overcome. No power coupled with a mysterious rev limiter. A Busted up cat generally rattles unless the broken bits get blown into the muffler and/or wedged in the cat outlet.
If you aren't getting bogging, I would take another look at the choke. The electric choke on the Carter uses a single wire to heat a coil, causing the coil to expand and thus open the choke. The wiring could be bad or the choke coil may be on it's way out.