Contradictory info
i wasn't that ready to tamper with honda's engineering quite yet without a good reason
Yet you changed the needle clip and the main jet. That was Honda engineering, too!
The F model clip position was 2nd groove from the top. So, you went two steps richer on the throttle valves.
You still haven't mentioned your idle screw setting. Here's why I want that info...
10 or 15 years ago, I bought a new gadget; an exhaust gas analyzer. I did a tune up to the 550 and at the end of it stuffed the analyzer up the exhaust to measure hydrocarbons. Then I adjusted the idle screws for lowest levels at idle. Purred like a happy kitten on the centerstand. But, I wondered why all the idle screws were at now at 5 turns out. How could the manual setting be off so far?
The test run gave the immediate answer. Throttle changes more than 1/8 turn just made the engine wheeze when under any load. I didn't get 50 feet, before heading back to the garage for a screwdriver. I proceeded to turn each screw back in, in half turn increments, and then driving a few feet for effect. Response improved steadily, and when it got close to it's old self I changed to 1/4 turn increments, and then 1/8 turn increments. This process repeated until I had the throttle response I was used to having with the bike, and an additional 1/8 turn made no response improvement. Turned them back out 1/8 turn for a "peak" setting. Back to the garage I wondered what the optimal setting ended up being. Counting turns I found them all to be at 1 and 1/2 turns. I checked the book spec. again; 1 1/2 turns.
Who could have guessed that Honda knew how to adjust their bike?
This 74 CB550 is has the stock 4 into 4 and airbox. However, I do have A Uni oiled foam filter instead of the stock paper type.
Maybe, just maybe, your exhaust and filter changes require you to find a new idle air bleed setting?
Plug color:
To my mind, light tan is is where you want to be. Chocolate, while yummy, is in the too rich range.
Missing from your description is if that is a general color, or a fixed throttle position plug chop result.
( You could, in theory, have a rich slow and wot setting, and a lean midrange setting, or other combinations, to average chocolate brown plug deposits.)
Low speed throttle response:
I don't think you should ever be able to snap the throttle open from idle, without the wheeze response. 1/2 to maybe 2/3 yeah. (No accelerator pump and no CV). You'll be slobbery rich if so.
The physics of the slow jet orifice is tied to barometric pressure difference between carb throat and surrounding atmospheric pressure.
The filter material before the carb inlet effects that pressure differential. Materials that allow high flow at high inlet speeds, offer little resistance to flow at low speed as well. And, this creates less of a pressure differential in the carb throat at low and idle speeds when compared to surrounding atmospheric pressure. This means a 38 slow will supply less fuel with low restriction filtration, even though at 1000 RPM the engine requires exactly the same volume of air to sustain that engine speed. The air bleed screw should be able to adjust the mixture ratio correctly, but the total volume supplied may not be enough when the slide is opened and the throat baro pressure raises significantly. Think accelerator pump simulation. I'm thinking that your bike with pods probably ought to have larger slow jet orifices. Find some 40's or 42's, perhaps, then retune your air screws for mixture and throttle response from low RPM.
i am gearing towards low end city driving power and willing to accept a loss at cruising speeds
It seems odd that you chose pods, then. Pods are for breathing at high RPM. Seems like you've chosen the wrong tool for the job. The assemblage of components is the result of design trade offs toward a specific goal. There are few components that do all things for all functions and conditions.
Lastly, your "stumble-wheezy-intermittant" problem. Start tracking the local Barometric pressure, to see if there is synchronization with the intermitantness along with engine or air temps.
You did ask for "thoughts", yes?
Cheers,