Is the kickstart hard up against the outer cover?
No, maybe an 1/8" shy but I would need all that to clear the recess if I were to drive it on further.
1) Be sure that the bolt and lever go together properly in with the lever off the bike.
2) Be sure the lever will go on the shaft all the way to touching the case.
3) Quit looking at the gap and see if the bolt will go in with the lever on the shaft.
a. If so, don't worry about the gap if there is a tiny one after kicking a few times.
b. If not, check the lever hole and bolt diameter. I've had to SLIGHTY radius the edge of the slot in the kickstart pinion for those levers because they can catch on the slot in the shaft - it's only been the top outer edge that would interfere.
Keep in mind that with no shims, the shaft can move in and out quite a bit. Since you have it all together, it doesn't seem so because the spring makes it difficult to move in an out. There is nothing to firmly locate either the kickstart shaft or the layshaft. It is possible that your kickstart shaft is simply in too far and that once the lever is on and in use, that everything will align itself. I like and use those levers, but the hold placement is NOT accurately done!
And, you said: "maybe an 1/8" shy but I would need all that to clear the recess if I were to drive it on further." Driving it on obviously moves the kickstart shaft towards the gearbox as much as the internal slop will allow.
If you have a stock lever, try it and compare the two.
Of course, if you determine that the kickstart shaft is bad, send it back - as I remember it, it was like new, but I did not remove it from a gearbox so I cannot swear that it has no problem. Even new parts can be made wrong.