First off, make sure that you set the timing with the vacuum advance unhooked, and with the engine at or below the curb idle speed. If the RPM is too high, you may have some mechanical advance already happening in the distributor. If it is correct already, you may want to bump the timing up a few degrees. It won't hurt anything, but make sure it still cranks over and starts when its hot. Too much timing can cause the engine to kick back against the starter, but a few degrees won't hurt. Also, drive the Jeep and make sure you don't get any pinging. This will hurt an engine over time.
As far as the carb, if it wasnt properly recalibrated for the altitude, your engine is probably running a bit rich. I would recommend dropping a jet size or 2 and reading the plugs. They should be colored a light brown or straw color.
Chris