@Seancb750, I'm going to take a guess at this. Let's start with some background. These DOHC engines are much more efficient than others due to the YICS system. They require much less fuel than others, even compared to the SOHC engines. Due to the smaller throat in the carbs you installed, that were jetted for a less efficient engine, my
guess is you are running excessively rich above 1/4 throttle. Apparently to the point of not being able to rev the engine. I'd expect black smoke from the exhaust. If so, that would be the diaphragms, needle jets and jet needles, and float levels. Again, this is a guess on my part and you will need to prove (or disprove) before going any further.
It is also possible that your TCI module is failing. Using an inductive timing light, you should be able to verify if the ignition is functioning at higher RPM or if it is cutting out. Replacement modules must have the exact same model number. I've only found used ones, and they were more expensive that I thought reasonable. They are reasonably easy to rebuild for those with average soldering/electronics skills.
If you are in agreement with my guess of running rich, start your tuning by tossing the pod filters in a bin, having your mates piss on them, and then throw last weeks leftover Chinese takeout on top. That should prevent any temptation to recover them. Pods are NOT for CV carbs. If that is too much, or you have no other options for air filtration, make some stacks to mount the pods to. Trying to tune with pods directly on the carbs is a waste of time. I know, I wasted a year trying.
Once the pods are dealt with, inspect the diaphragms and lower the needles as far as you can. If the needles don't have multiple grooves, don't waste any more time and go find the correct carbs. Also, reduce the main jets to 120, and lower the fuel levels to 4mm below the body. Hopefully that will get close enough that you can ride the bike and do some fine tuning.
Good luck and keep us apprised!