The smaller question is, does this sound like a good base jetting for a stock 78 CB550K engine? I know the chart I posted shows leaner jets for the later years but was that based on performance or trying to curb emissions? It seems to me 100 mains and 40 slow jets would be a good performing baseline to tune off of.
You're right. The CB550K3 was much critisised for running a bit too lean. This was to curb emissions.
Orrrrrr should I just leave the 100 mains and 38 slows in there, give everything a good cleaning and tune and just go from there?
Yes and consider yourself lucky you have the oldstyle Keihins and not the later PDs that are much harder to work on.
Now that you've pulled the carbs, it is a good opportunity to clean them. There's no need to separate them from the rack and there's no need to open the tops. So don't.
Here's what I would do.
1. Have little boxes 1-4 or jars ready, so you won't mix up the brass parts.
2. Remove, inspect and clean if needed floatpins, needles and seats.
If you use small pliers (better not) to extract the floatpins, do not pinch them and do it gently. Some manage to break the towers. A little WD-40 at forehand may help. Check these parts carefully. You may polish them but... a little.
3. Unscrew slow jets (aka pilot jets) and inspect them. These are the jets that are most likely to get (partially) blocked when the bike is not used regularly. If you do not operate the bike regularly, you may need an additive to the fuel to keep the fuelsytem clean. You may soak these jets in a little carbcleaner. You can clean them with stranded copper wire or anything as long it's not harder than the brass it is made of.
4. Pull the main jets. They are easy to inspect and clean. Do not forget to inspect the small O-rings around them. When in doubt, replace!!! It's very important they'll seal well.
5 Now, with the main jets removed, it's easy to pull the needle jets aka emulsion tubes. For that you must bring the carbrack in the full throttle position in order to raise the needles inside (you will leave them and the slides where they are btw). When the needles are high up, you can pull the needle jets. Sometimes they fall out spontaneasly, sometimes you have to help them. You can use a matchstick or wooden toothpick and insert this from below into the tubes. By canting it and some wiggling you can pry them out. Spraying some WD-40 at forehand may help. Inspect the little holes in the tubes. You may find there's white stuff in them. These holes must all be open.
5. Remove from the sides of the carbbodies the airscrews and clean them. Do not loose the little springs.
6. Now spray carbcleaner in all the orifices of the carbbodies where you have removed parts. After a while repeat.
7. Note that the pilot circuit has no less than four orifices: 1. where the slowjet sits, 2. where the airscrew sits, 3. the tiny little orifice in the throat of the carb engineside just in front of the slide and 4. the opening in the mouth of the carb as shown in the pic below (pilot system air jet). Check that carbcleaner comes out all of these openings.
8. Check that carbvent openings (and attached tubes!) are open.
9. Check fuellines for appropiate length and diameter.* No kinks, no extra inline fuel filters.
10. Reassemble.
This is it. It's also a good opportunity to check the operation of the chokes and you may consider to renew the four 30,8 mm O-rings between the engine and the manifold as they often become hard over the years and will leak as a consequence.
*
On the bikes that originally had these carbs, fuel lines standard length were 18 and 30 cm with the oldstyle petcock and 17 and 28 cm with the new type petcock. Ideal diameter is Ø 5,5 mm.