Too bad about the pilot fuel screw tips. Hoomgar, a member here, made a good thread about removal, so I'm a little surprised you couldn't get the one out. I hope your new set of carbs will be good. I used to rebuild carbs for extra spending money and you really have to ask lots of questions to try to avoid receiving carbs with more problems.
I'm against running the stacks but I'll try to suggest jetting that will work. It's very possible that your re-jet will have to be done again if you decide on some K&N's later. That means not only main jet changes and possible pilot jet changes, but possible jet needle adjustments that mean taking the slides out again. And every time you disturb the jet needles on VM carbs, you must re-bench synch and then re-synch with a vacuum tool. Personally, I wouldn't use my time and possibly re-jet/re-test twice. If at all possible, I'd get the K&N ovals (P/N- RC2454).
This brings up another $ issue...a jet kit. If you've read any of my past posts on re-jetting for 1085/V&H/pods, you'll see that the stock jet needles SOMETIMES just don't allow enough richness. That's why I come right out and suggest the DJ jet kit. I'll make suggestions for your stacks and stock needles but at least you've been warned that your efforts may not work. The stacks make it more likely the stock needles won't work, but what helps a little is the typical higher humidity you have there. I'm no expert at your actual weather, just things I've heard about it.
I suggest a look at the VM carb series clean up/rebuild section here. If you don't have the factory manual, this section is helpful.
When re-jetting, I always follow a strict list of things to do to make the re-jet easier. One of those things is to replace ALL inner o-rings. Robert Barr, a member here, sells a very good o-ring kit for the VM carbs. I recommend it. Don't re-use older, hardened/brittle o-rings.
Be very thorough when cleaning. Verify every tiny hole and passage is clean. I use high pressure air after soaking/cleaning and I verify that air passes in and out of every passage.
Don't mix the carb parts. Keep each carbs parts with that carb, especially the float needle valve and its seat and the jet needle and needle jet combo.
Set your float levels right in the middle of the factory recommended range of .90" to .98", that means .94". You may have to slightly tweak the floats a bit to be sure both sides are even with each other.
Be very careful that every part goes back in the right side up and in correct factory order. The thin brass plate that sits under the throttle arm base (between the base and inside of slide) is sometimes installed upside down if you didn't pay attention. Note the little raised dimple on it. When making jet needle e-clip adjustments/re-assembly, be sure the two plastic jet needle spacers go back in correct order...thicker directly on top the e-clip/thinner under the e-clip.
Don't over-torque small hardware. 3.5 ft/lb for the throttle arm-to- throttle shaft bolts. 3.5 ft/lb for the holder nuts that hold the synching screw on top of the slides.
You say the valve clearances, ignition timing, manifolds are good.
Be sure of clear gas tank venting, correct 5/16" fuel line and good vacuum hose condition. Be sure the petcock is clean.
Be sure the plugs are NGK B8ES, gapped at approx' .027/.028" and all leads are in supple condition. Coil lead to plug cap connections must be verified solid and tight and clean. Spark should be a good bluish/white color.
As a side note, inspect/clean all electrical connections. The wires from the stator are often over-heated due to the poor design of the stock reg/rec. The rubber boot that holds a wire bundle right by/above the battery, often has burned connections in it. Check your electrical system. Read the Stator Papers here to understand why you may want to install a superior R/R, if you see any problems. Pay extra attention to good grounding of the system. Install the extra grounds, etc.
A bit of work, but if all the above is done first, then any performance problems will be jetting related and that makes things easier to adjust.
I'll get back with the jetting in a bit. Got to eat supper!
