It is easy to tell if that weber vacuum source is ported or manifold (I know some carbs can put ported right at the base and fake you out)--if it has any vacuum at idle (without the throttle valves open), it is manifold. Ported vacuum will be zero at idle and only develop as the throttle is opened. I'm not pretending to be any kind of expert on this stuff, but if you put in a new cam, you could have easily increased the compression in your engine and affected the proper timing considerably, so I wouldn't necessarily say that there is anything wrong with 12-deg (or more) if your engine is running well with a lot of advance. The pinging may be the result of using too low-octane gas if the engine is now producing more compression. The difference between 87 and 89 on mine would amaze you, and you may need at least 91. Stumbling can also be an accelerator pump adjustment problem within the carb, so make sure that it is adjusted as best as possible. My carter had a terrible flat spot just off idle until I got it just right. Don't know if this stuff will help--just my 2 cents. Concerning jets, I know that some motorcycle carbs have to be rejetted when they go to straight pipes to keep them from running too lean (hot) and bluing the pipes (my little bro ran into this on his Softail), but if you have anything more than header/scavenger pipes, etc., you should have enough backpressure to not have to worry with that. When you say "straight pipes", do you mean not even a muffler? I guess on a CJ5 with no muffler and those short pipes that exit by the door openings, maybe you could be a little bit lean--don't know that one for sure.
Currently an '86 CJ-7 and a '77 CJ-7 Golden Eagle---#4 and 5 following a '01 Sahara, '90 Sahara, and '85 CJ-7....