ULS Carburetor sync

I did take both the chokes apart to change out gaskets and o'rings and I double checked that they went back together correctly.  I usually have to give it a few seconds of choke on an initial start of the day but not on subsequent starts in the same day.  I have a T handle turn-to-lock choke lever but rarely use any choke after it starts or while the engine is warming up.  The chokes seem to be working fine.

You say the chokes are "working fine", but you did not answer my question about what position each of them is actually in.  The position of the activation handle is not the same as the position of the chokes themselves.  Cables can get hung up, etc.  If one choke remained engaged and the other not, that could cause a big imbalance, and unintentional (even partial) choke engagement could in itself go a long way toward explaining the roughness you have described.

Did you work on each carb separately?  I have heard tales of people that swapped chokes and never realized it; they are not interchangeable.

Yes - excellent point and I would love to find that this is the underlying issue but I'm very sure that I got both chokes back together in their proper orientation per the applicable figure 73-25 of the heavy maintenance manual, and I have also double checked that they actuate and release properly when the cable is pulled and released.  Although my older choke shafts are not physically marked with an "L" or an "R" as shown in the figure I do realize that the two chokes are not interchangeable and there is a left and right config (one for cylinders 1/3 and the other for 2/4). 

On your question about throttle stops. The McFarlane throttle comes with throttle stops. They are a small barrel like device with a set screw in one side a a hole for the cable. They install on the cable where the center cables comes out right at the cable adjuster installed on cable just before pushing cable through the throttle arm.

https://skygeek.com/mcfarlane-aviation-6270-control-cable-stop-assembly.html?utm_source=googlebase&utm_medium=shoppingengine&utm_content=mcfarlane-aviation-6270-control-cable-stop-ass

Larry Olson wrote:

When I overhauled the carbs I didn't touch the main jet needle and clip because I assumed that it had nothing to do with the idling of the engine and the clip must have still been in the slot as installed by Rotax when the engine was new (no one ever moved it since).  Is it possible that it could impact the engine at the lower rpm range that I'm running at and is the clip position critical to this whole discussion?  I don't remember now which slot the clip was in when I replaced the rubber diaphragm.

If this main needle and clip isn't associated with the idling issue I'm now seeing I will no doubt take the carbs into my nearest overhaul facility and have them look at it (LEAF is within 85 miles away).

On thing thing needs to be done when working on problem carbs is the inverted float needle valve test per section 73 in the Rotax manual. Not doing it is just guessing..  Making a test rig is buying a cheap electric fuel pump, pressure gauge, fuel line, shut off valve and the hose barb, spacer to connect hose to carb. I spoke with one independent Rotax repair center (not Leaf) that overhauls carbs and does not do the test. Sends them back to you to find out if the float needle valve leaks and ruins your day. Some of your issues sound like needle valve may be some of the problem.  I just went through all of this on my Rans S6.