The accelerator pumps were put on larger engines and larger Carb bores to overcome the lean burn idle many machines were re-tuned to provide for EPA concerns. Previous engines and smaller ones relied on over rich idle mixture settings to provide engine response from low throttle positions. Carbs without accelerator pumps can not accept snap open throttle with out a major wheeze response. However, throttle position changes of 1/2 a twist should result in good, smooth engine pickup.
I suggest you temporarily mark your twist grip so you have a positive reference about just where the throttle is when you have your performance issue. Depending on where your throttle is positioned, 1 of 4 metering devices in each carb determine the mixture delivery; slow jets, throttle cutaway, slide needles, and main jet. The throttle cutaway is not normally adjusted as you actually have to add or remove metal from the slides. But, these have a dominant impact on mixture during the transition from the slow or idle fuel metering device to the needle jet system.
Dark brown is an indication of over rich, but unless you've limited your run time to specific throttle settings, knowledge of which devices are causing rich or lean conditions is unknown. (I'm going to assume you are reading the correct part of the spark plug and they were clean before the most recent test.)
Lastly, the idle air bleeds often need a different run position when change exhaust or intake components, as the factory found our where that setting was appropriate with those run conditions. The air bleeds either add air the idle mix or restrict it. If they are set too lean, powered pickup from idle or near idle setting will result in hesitation and a "wheeze" before the bike accelerates under throttle changes of 1/2 a twist. If too rich it might burble with acceleration, but it might not as much more fuel is required for accelleration. However, if you can snap the throttle open and accelerate smoothly it is definitely too rich at idle.
To find the idle screw settings that match your configuration, do this. Begin with factory settings, drive the bike and note engine pickup response to throttle in gear from near idle RPMs. Now open the screw 1/8 to 1/4. You should find that the driving throttle response is more sensitvie to how much you've changed the throttle position. If not, open the screws some more. At some point in this re-iterative process, you will find that throttle response is so dismal you can't stand it. You've gone too far, then and should turn them back to where you are happy with the smooth pick up provide with about 1/2 a throttle twist from idle. It is possible that your new idle screw settings could be less, more or even the same as the factory specs. But, with engine breathing changes, you don't know until you find the sweet spot for the new setup. This may or may not fix your cruise/throttle issue. But, it does address one metering device in the carbs.
One diagnostic technique is the temporarily removal of the air filter to determine if conditions in your problem area improve or worsen. The partial choking effect provided by the air filter is removed and leans the mixture some. Conversely adding partial choke enriches the mixture. With these two diagnostic tools and reading spark plugs, it should give you a good avenue to approach making carbs changes in the correct direction.
Cheers,
