99 kawasaki ninja EX250 motor swap for a 98 NINJA EX250 MOTOR

Here is a good You Tube video on adjusting the valves, which is really what you want for proper timing, which was advanced for this model. Classic Ninja 250 valve adjustment procedure tutorial

sounds like you have a carb problem Jason,possibly probably your float level is set too low not allowing sufficient fuel to Venturi

Go to this web site, it has almost everything you will ever need to know about your EX250. The people there are very helpful and very knowledgable.
http://forums.ninja250.org/

Beside the fuse box

cyclepedia.com/kawasaki-ex250-ninja-250-online-service-guide/
ebookoo.net/the-kawasaki-ninja-250-faq.html

i feel the above links may be useful for you

Bad contacts on the battery posts from corrosion can rob the spark of 40% of its power on start. Make sure the battery is fresh with a good overnight charge and make sure the posts are really clean. You may also have a bad voltage regulator. I keep a spare in the garage so I can swap out a part I think might be bad. 11 years on the old one could mean time for a change....

If you can't find another similar connection on the new motor, you might need to swap heads (if it's the same exact motor).