Not sure I understand how a manifold leak could possibly be causing a lean condition when the throttle is whacked. It's pretty obvious that you have a giant vacuum leak caused by whacking the throttle and it's right through the middle of the carburetor. The big issue is that velocity air is to low and there is some delay for the main jet to start feeding fuel past the needle/ needle jet orifice..

If you want to fix the issue you need to be looking at the accelerator pump and needle jet / needle / emulsion tube. 40CVs are designed to run lean for emissions and the stuff listed has been tweaked to help do so.. In the process, I'd expect that the fuel mileage will decay.

I'd go for the accelerator pump first then since you tried raising the needle, try more or try another. I would not sand the needle. They are hard anodized to last. Go through the anodize and the needle will wear. Maybe open up the needle jet? If doing so you only want to do steps of about 0.001" at a time. Mik needles step in 0.01mm so it's about 0.0004" They have more effect though as miks don't have emulsion tubes. You can also try filling the 2 of the upper holes in the emulsion tube with solder.

 

The Mikuni is a lot more tunable but there is a learning curve to it.
Pick up a needle for an '88 Sporty. It's an N65C.
It's been long discontinued from Harley but CV Performance picked up making them.

CVP N65 Needle

 

Just to report back, since most OPs never seem to: Drilled the slide to 7/64" didn't seem to change much. The biggest improvement (purely in terms of AFR numbers) seems to be from shimming the needle way beyond what is typically recommended, but of course this leads to a fairly rich idle. Will look at different needle tapers and jetting combos in the future.

In any case, I stopped experimenting with it and threw on a Screamin Eagle Holley that I've been wanting to mess with. Yes, I'm fully aware that this goes against the advice most reasonable people would give, but I figured I'd just go back to the CV if it didn't work out. I'll make a separate thread in the appropriate place on the matter, but long story short: the Holley is a different animal with a big learning curve, but it sure does look and sound good!

 

That N65 needle is what you need.

 

 

Go back to a smaller pilot jet?