the only thing I can comment on is the mods you made to the airbox
the carbs need the airbox where it is and like it is because the carbs create a standing pulse of fuel/air fog in the air box when the engine is running.
If you cut the airbox open and stuffed some airfilter in there, you have changed the dynamics of the airflow on the intake side of the carbs.
To explain this another way, if the shape and volume of the air box was not necessary, there would just be a tube or hose going from the intake of the carbs to the outlet of the air filter enclosure. The airbox space and volume is necessary.
People make the same mistake when they try to run or test or tune the bike with the airbox unconnected, or when they put those cool looking air filters right on the intake of a carb. The engine will not run right if there is no place for that standing pulse of mist (where the airbox is suppose to be, with nothing in it). There are some really terrible videos on youtube about modifying and maintaining your motorcycle, some of them will outright cause you to destroy your engine or damage other parts of your bike, and there is no one there to correct those videos or force youtube to take them down. A lot of bikes end up being basket cases as a result.
you said the airbox mod and new jets made the bike bog down, and you rode it that way for three years. What did your plugs look like after riding it that way, lean - rich - or normal?
Im afraid you have ventured into a sort of no-mans land: you made some mods to your motorcycle that are not standard or conventional, it was running but was a bit off, then you took it to a regular mechanic to do the starter clutch repair, with things only finger tight and the spark plugs not torqued down or plugged in all the way. When this happens the mechanic does not know what you have done to the bike, so when its not running right he cant assume what has been messed with or altered and what is still stock.
If you step back and look at this from the shop mechanic's perspective, the bike was not running fine when you took it in. The starter clutch had failed, the plugs were not screwed in, it was not running at all. The mechanic never saw the bike running when you took it in - just trying to be fair on both sides. after the mechanic fixed the starter clutch "they called and said the starter clutch was done but the bike was running poorly". He knows how the bike is suppose to run.
Its easy to check the valve timing, you take the side covers off the heads and see if the timing marks line up with the timing mark on the crankshaft. The odds that an experienced mechanic would replace the starter clutch and jump the chain on the valve timing are pretty slim, but again that would be an easy thing to check.
I would seriously consider replacing your airbox mod any of the aftermarket intake pods that have a proven track record. Then you will know what jet sizes are needed for that intake and your aftermarket exhaust, and how far to turn the PMscrews out as a starting point to tune the carbs for the aftermarket intake pods and exhaust.
I hope this does not sound like Im being critical of you personally. Sometimes people make mistakes or do things on their bikes that cause problems. If we focus on the issues with your bike Im sure we can help get it running perfectly.
I have to add: there is nothing wrong with trying things out, experimenting on your bike, trying things to save money when you need to, and finding clever ways to make your bike run better. The thing is you have to be willing to make mistakes, and sometimes to fail, and be willing to work backwards to find where it went wrong.
Last edited by KCW; 08-23-2019 at 11:03 AM.