Any idea which 4-1 headers I have then? Curious if these ever came stock on the 550 or if the PO bought them somewhere else.
Definitely not stock. I'd guess yours are MACs, as they are the cheapest aftermarket system available.
What I gathered by this paragraph is that a Honda stock 4-1 will be better for the street than a different "race" 4-1. And possibly...dare I say easier to tune? Or at lease give better results. Although maybe not because I'm changing the muffler from stock...
Let me introduce you to the concept of "systems".
The header and pipe make up an exhaust "system". Technically, the exhaust valve, its timing, and port characteristics are included in that system.
If you change a part in the system, the behavior of the system changes overall, and the tuning changes vary in unpredictable ways unless you know what the characteristics of the components within the system were before and after the change. In the stock muffler case, there are pressure characteristics, as well as baffle impulse reflection distances from the exhaust valve to consider. An aftermarket muffler is unlikely to replicate those parameters on their build-to-a-price-point offering.
The stock systems are easier to tune because Honda did all the characterization for you, and made a "recipe" to fit the parts of the system.
Change a part's characteristics and you change the recipe. Restore to fit the recipe, and it works as originally predicted without much bother.
I feel comfortable in saying the MAC exhaust components, are built for easy, quick, and cheapest assembly parameters. Pipe diameters, baffle reflection points as well as overall pipe pressure level are whatever happened to be assembled on the day of production. Their part control measures are likely limited to a fixture, that holds the pieces in a position where they can fit on the bikes they intend to have them fit, and the overall end product looks like what they show in the catalog (very artsy!).
Any other advice for a starting point as far as jets go or the above posts are as good a place to start as any?
You mean without knowing which exhaust you will eventually choose or it's characteristics?
OK then, a W.A.G. Main jet; 100-102, Slide needle; 2nd clip position from bottom, #42 pilot jets, IMS at 3 -4 turns out.
I know you wouldn't do this at all, but if you could imagine you were a suffering art projecteer you'd do what? After a little wax poetic, that is.
Actually I might do this. ...After an apocalyptic event that made proper parts unobtainium.

I was thinking about your statement that you wanted a finished bike that was unique and could call your own as original. ...And the thread begins with asking tuning advise from someone whose has the same set up.
This forum is a hoot sometimes...

*Maybe I'm nit picking but I might feel a slight hesitation right off the line.
IS this occurring with what induction and what exhaust?
Anyway, the symptom description is that of classic too lean an idle mixture (caused by a pods change and/or loss of exhaust back pressure), possibly cured with more outward turns on the pilot screws. However, the slide needle and main jet "leak" a bit at idle and larger orifices do have an effect on idle mixture. Another adjustment to have an effect over all throttle positions, is the carb float bowl fuel level. 12.5mm brings the level upward and makes fuel enter the throat chambers more easily.
The rejet carb process is best begun with determining the correct main jet size. This sets the maximum flow required for the engine from the carbs.
The two extremes are min. and max. The pilot system sets the minimum, and the Main sets the maximum. The slide needle addresses the throttle positions in between.
Mechanical slide carbs (without accelerator pumps) must be over rich at idle, as they naturally lean when the slide is first raised. The slide raising not only makes more air available, it also allows outside air pressure to reach into the carb throats. Since it is the differential pressure between what exists in the carb throat and outside air pressure that drives the fuel into the carb throat, reducing the differential pressure reduces fuel volume at the same time raising the slide makes more air available to the intake. The result: stumble. The cure: make the pilot mixture over-rich and limit the amount of throttle twist from the operator.
The 77-78 PD carbs were very stingy on the pilot mixture to meet EPA exhaust sniff requirements. The high pressure exhaust was used by Honda as a way of reburning hydrocarbons left over from the previous burn cycle. Reburning allowed this otherwise stingy mixture to idle and accelerate smoothly. Change the 77-78 high pressure exhaust to a low pressure system and the stock carb instantly provide less than needed fuel from the pilots, effectively leaning the idle mix and inducing throttle twist stumble. PD carbs with the 42 pilots should have enough adjustment to restore over rich idle (much to the chagrin of the EPA and the majority of breathing mammals). I'm not so confident about the PDs with #38 pilots, but it is worth a try to simply tweak the IMS.
Note that you may have to also stretch the pilot screw springs to keep the pilot screws from vibrating out of the carb body.
It is assumed that the bike's ignition system and valve adjustment are in proper working order. And that the carbs are vacuum balanced for the engine.