Maintenance first! tires, chain, bearings, oil,ect...... if your broke down the mods aren't going to be any good.
For me make is easy to operate. If its a bear to ride riding will suck!
1. Raptor 350 clutch cable upgrade
2.Direct shifter setup
3. Front suspension install Banshee front shocks if you want a softer better performing ride.
4. Rear suspension two ways to go
Banshee rear some air box mods needed
2001Raptor 660 only year to fit no mods needed
Search "Yamaha front shocks" on eBay you can find Banshee fronts all day long in the $50 range.
Rear shocks are a little more pricey.
Engine:
1. Good breathing air filter system.
2. Camshaft hotcam ect...
3 Vito's flywheel advance key
Tires:
1. Sky's the limit here there are so many
Just choose the correct ones for your riding environment.
If its just pure mods you can go radical or slightly modified, it's up to you. But rest assured you have come to the correct place for advice and ideas.
One note of caution, steer clear of "I think" advice. There is quite a bit of solid information if you just use keywords in the search box.