You realize you are asking me for a 1000 page book right? I took 45 years to amass what I personally know about the subject.
You don't generally ever rejet for idle, the idle is adjustable enough with the pilot screw and why most Hondas use the same or virtually identical idle jet over a wide stream of engine sizes. 35, 38, or 40 and 40 is often too big, they are all close to the same jet. High perf parts do not generally affect idle as the actual air entering the engine is so small in volume. Usually another half turn on idle mixture to richen and you are there but you need to know if that means further open or closed, there are idle systems that are backwards of others.
I have a 550F that has pods and a much more efficient muffler on the header and only went from say 120 to 130 on main alone and it runs perfect. Sometimes you need to lift the needle up one step to help mid range after you do the main. I rarely do here in Texas, it may be needed if up north where air is generally colder.
If anything runs richer after engine changes but before the rejetting you DECREASED power there with your mods. Happens all the time. Or engine has something wrong with it. A non-OEM 4-2 can do that if it uses a crap design internal baffle like some Chinese stuff uses. Pods can do it if the engine really liked the tube extension from the carbs to the airbox, the early DOHC does that. The pods shorten the effective velocity stack and then engine tune goes off. So then people are convinced they need the jet (because 'everybody else says to do it'), add it and then bike runs like crap when it wanted LESS fuel not more. Then not reading plugs leads to adding even more fuel because owner cannot grasp the reverse idea and bike pretty soon for sale with carbs off of it. I've gotten two free DOHCs that way. Both running fine 30 minutes later when they would even start before. Owners totally lost and plugs fouled out. Bought a $1000 new RM Suzuki once for $300 that wouldn't run and maybe 30 minutes on it, Suzuki made an unannounced factory needle jet change and the guy modded by changing the expansion chamber and jetted up and bike refused to run. I found the running change and dropped main jet DOWN about 20 numbers and bike instantly ran to 10,000+ rpm after a plug change. Sold it for $800 4 days later.
You need to learn to read plugs, the only indicator you have of whether you are helping or messing things up worse.