So the 96' Honda CBR 600 F3 I picked up doesnt have keys. Should I get a lock smith to cut a key or should I just change out the ignition system for a new one with keys, which can be purchased via ebay for under $40

 

if you get a new ignition, you would need to also get a new gas cap(and would have to drill the lock out to get the old one off), and new helmet lock.
you can get all 3 off ebay for around ~$90. But id see how much it would be to get a new key cut first.