Hi Curt mate......
I'm no mechanic and someone with more knowledge than me will be along soon with some concrete advice but the battery you have should be upgraded asap to a 12ah one, the bike should ALWAYS, ALWAYS be plugged into a battery conditioner/trickle charger and lastly, change the starter solenoid for a Yamaha one (search this forum for the exact part number). If it don't start VERY soon after thumbing the starter WALK away from it till you have charged the battery fully and try again, continuing can and very possibly WILL f*ck your sprag clutch, which i've been advised is a costly repair!!
The chip and filter shouldn't cause this grief i don't think bud.
Hope this helps and you get it all sorted soon................:thumbup