Welcome to the site.
First off, you do not put any oil into the crankcase. The reason you blend a lubricant with your fuel is to lubricate your rotating assembly's bearings and seals which are found in the crankcase.
I would change the transmission fluid and coolant right away.
Go over all suspension, steering, and brake components. Grease all that can be greased and check every bearing, bushing, joint, and pivot point for tightness and wear.
verify the compression of each cylinder.
perform a plug chop to ensure proper jetting... address the jetting if it is incorrect.
Pull all electrical connections and dab with dielectric grease.
Buy a clymer's repair manual and perform a complete tune-up.
Also, you have R2 pipes. They are nice pipes (what I run). Tom Borrink does not stamp any logos or identification onto the pipes. As for jetting they seem to like a leaner pilot jet compared to other top end pipes.