What is the best mod for under $100 for more bottom end?
So far I have a FMF fatty pipe and PCII silencer

 

For low end, I would think new reeds and a reed spacer? Maybe a smaller front or bigger rear sprocket, I just installed a 12 tooth front and its more power, but slower.

 

Reeds $50.00 '89 CR250 head gasket $17.00(+ materials)& two base gaskets ($14.00), requires you to be on top of your jetting and run premium gas.

 

I must concur with BACKCOUNTRY! A bump in compression(CR head gasket) will definitely help lowend. Reeds will also make a big difference. Eric Gorr recommends Dual Stage or .4mm fiberglass to help a LOW-MID bias. Go to www.eric-gorr.com/tech/egportweb.html for a great article describing what components to change to affect a two strokes powerband titled "How to Choose a Powerband". It's VERY IMFORMATIVE!!!