Oh my! The easiest problem to solve ;D.

I was once a victim of this atrocity. My computer hadnt crashed for ages, and in retrospect, i gained lots of levels. The thing is, JJ2 dosent like it if people have OVER 256 levels (or a number similar to that). JJ2 wont run.

The solution is, to either delete files (LEVELS ONLY) that you dont like, or wouldnt use, or you cant get into because its passworded. Repeat as many times as needed. Lather. Rinse. Repeat.

Hope this helped ^^

Edit: READ THIS TOO! Leave in your music and tileset files (unless you hate them) because they dont take up slots in the homecooked levels menu.