John,
Definitely check those manifolds. I don't think anything was done to them, but better safe than sorry. Plus you'll be starting over on the sync anyway.
Syncing (somewhat abridged)
0. You want the motor nice and warm, because heat expansion can affect these settings.
1. Remove the linkage. Seat the air bypass screws completely (next to the idle mixture screws, 8mm lock nut). With the motor idling, check the airflow on both throats. Back out the air bypass screw on the throat that is flowing
less air. Once the two throats are matched, tighten the lock nuts and double check. Now repeat on the other carb, but
don't try and match the air flow on both carbs. This step just equalizes the individual carbs and must be done correctly before moving on.
2. Using the idle adjustment screws (by the linkage, not the mixture screws) to match the air flow between the carbs. You'll also want to get it roughly idling at the correct speed.
3. Now reconnect the linkage with the motor idling, and make sure that your linkage doesn't change things. Adjust your drop links as necessary to maintain the correct airflow. You don't want your linkage holding anything open when it shouldn't.
4. Shut down the motor and check that both carbs are hitting WOT at the same time (or at all). You may have to adjust the location of the arm on the hex bar in order to get both idle and WOT at the same time. Don't worry about if you drop links are vertical or equal length or anything else like that. If you're getting idle and WOT at precisely the same time, then that's perfection.
5. Restart the motor and check the idle airflows and check the airflows off idle (what RPM doesn't really matter, but you'll need to have someone help hold the RPM up). Any discrepancy here must be adjusted out in the linkage geometry. Expect to go back and forth on the linkage geometry for an hour or so.
6. Double check all of the airflows on all four throats at idle. And
NOW you can start playing around with idle mixture screws to clean up the idle.
7. Triple check the airflows on all four throats and if they're off, go back to step 4.
If your idle airflows, off-idle airflows, linkage geometry (hitting idle and WOT), and idle feel/sound/vibe/mixture are all right, you can test drive it and see how that all feels and then start another round of tweaking. As much as you want it to be over quick, you'll get much more positive results by really digging in, assuming nothing, and triple checking everything.
Good luck!