Dynajet jet needles are long and thin with little taper. Stock Mikuni jet needles are more likely stubbier in appearance with more taper.
The bike was using aftermarket jet needles that are killing your gas mileage. Get a set of stock jet needles and toss the aftermarket. The second set of carbs likely had stock jet needles which were likely lean off throttle. The reason wasn't the jet needles but the pilot circuit. You will need a larger set of pilot jets (which never come in Dynajet jet kits). Adjust your mixture screws as well... at idle, adjust each in turn for max idle speed. Should be a couple turns out I am guessing.
In any case, once you get the bike to idle and come off idle OK after installing larger pilots, see if the bike will pull redline cleanly. If the mains are too small, it surely won't. If they are grossly overlarge, it surely won't. Ever hear of a plug chop? Make sure you are using Mikuni main jets. Start at a size where the results will be meaningful with your set up. If you are using K&N filters and a slip on, go up perhaps 15 points over the stock size... on a Mikuni main jet of #102.5 that would be around a #117.5. Then buy a new set of plugs in the correct heat range. Put them in your pocket and find a deserted stretch of road. With the bike warmed up, go to the side of the road and install the new plugs. Start the bike and open the throttle wide open in 3rd or 4th gear and try running at LEAST a 1/2 mile and then hit your kill switch and coast to the side of the road. If you can't get to redline, go as high an rpm as you can and sustain it for 1/2 mile.
Hit the kill switch, coast to the side of the road. The burn on the new plugs will reflect the air/fuel mixture at wide open throttle. Pull the plugs and if they are white, the mixture is lean and you will need to install larger main jets. If the mixture is black, you need to install smaller main jets. If the plugs are cardboard colored, the mixture is fine.
Once you have the idle and off-idle transition sorted and the correct main jets, fiddle with the mid-range. If your bike is baffled, you shouldn't have to make much adjustment, if any. If it lacks back pressure, then you MAY have to shim the jet needles. Mikuni makes .5mm shims which is about 1/2 a normal step size for jet needles with slots. I would guess you won't have to shim but could well be wrong. If you find a flat spot, usually between 4-6K rpm, then use two shims and see if that makes the flat spot disappear.