My son left for Iraq and his project KZ650 is sitting partially disassembled in my workshop. He was given the bike after it had sat for 1-2 years in a co-worker's backyard. He start tinkering with it and got the electric starter to turn it over but now it appears the engine is "stuck". I have decided to give it a try and have the pile of s*** in somewhat running shape when he returns. Any suggestions on what to do first?

I have worked on my own cars and trucks for 30+ years but have never tried working on a motorcycle.

PB Blaster is a good product for freeing up stuck parts, remove plugs spray in each plug hole, remove oil drain plug as you will want to change oil afterwards, plus the blaster won't remain in engine, let it soak in overnight, maybe less.
Electric and kick start turn engine 1 direction only.
I wouldn't use electric start until engine is free.
You may be able to put in gear and rock forward and back. Don't use excessive force.
Good Luck