You can start wherever you want to I imagine. I'd flush out the fuel tank, change the oil (use JASO MA - MA/2 spec'd oil only) and oil filter, new fuel filter, clean and restore the carb to stock specs per the FSM, check the timing chain, adjust the valves, adjust the clutch, clean the battery terminals and cables, clean the ground cable connections on the frame and motor, fix or replace the muffler, replace the brake fluid, check the tie rods and ball joints and relube them, adjust the brakes front and rear, check and relube the wheel bearings, replace the oil in both the frontend and rearend, lubricate and adjust all control cables, perform a compression test per the FSM (a dry+wet check) on a warmed motor.... by then you'll probably have any problems solved you thought you might have... and had so much fun working on your machine that you'll wish you had another one to fix up...
