I was in the same boat you are in a few years ago. From 2008-2010 I had a 2005 Sodikart (built for D1 tires but they had just switched to the D2) and was anywhere from .6 to a full second off the pace on a 23-second track. I was miserable. I bought the kart-engine with a fresh rebuild, top and bottom. Didn’t have a weather station so I either asked my competitors what jet / pin setting to use, or simply guessed. No one else ran that chassis. Always had used tires (I frankly don’t think that made a lick of difference to my lap times, as most of the time my competitors were on used tires as well). I did have the chassis on a scale so I was sure it was straight. I had my competitors drive my kart as well, but they weren’t any quicker.
In 2010 I bought a new Arrow AX-9 (another kart built for the D1 tire) and things improved, but only slightly. Got to within .3-.5 of the quick guys.
Finally, Rotax died at my track so I switched to Yamaha–and was immediately on the pace. So what was the deal with the Sodikart-Rotax? As with most things, it was probably a confluence of factors. I will list them in order of their significance:
1) I needed a driver coach at that stage of my karting. I perhaps still need one.
2) The chassis had not been tested effectively. Sure, I practiced and tested occasionally, but had little idea of how to make progress. Now I have a Tonykart, and to this day I usually have settings close to factory, and change very little during the day (mainly tire pressures).
3) I did not use any resources to tune the carburetor. Just cleaned it and guessed on jetting.