Depends on what altitude you ride at. For sea level to 3000 feet the most you might have to do is drop the needle clip one groove and see how the bike behaves. In rare instances you might have to go one size richer on the main jet.. Generally you do not need to touch the pilot jet at all.
You weren't born knowing this stuff.
I found the stock jetting on my 1998 KLX300 to be just fine for those mods and riding in Ohio. I would recommend the crankcase breather kit from Stroker to go along with the mods you've done. You should make sure you have the needle from a 1997 or 1998 KLX300. I heard Kawasaki went to a leaner needle beginning with the 1999 model year.
You said you cut out the backfire screen and removed the "end plate" I assume that you
mean the spark arrestor tip. Did you alsoopen up the airbox as well? If not I would recomend this ( I modified the opening on the lid so as to keep some protection to the filter).
The best thing is to ride the bike and check your plug so see if your running too lean or not, Make sure you have "broken in" the engine first.