Not meaning to slam you but your post needs some clarification before you can expect some help. #1 WR 250 what? R/X or F?. #2 What do you mean by dragging clutch? If your clutch is engaging in neutral have you checked your cable and lever freeplay? How many miles on the unit? Are you the original owner? How do you ride? What leads you to believe you have a dragging clutch? #3 On free mods, I do not think there is anybody who has posted that they reversed or wished they hadn't performed the usual free mods. They mostly consist of bypassing or deleting things Yamaha had to do to make the bike legal for sale; i.e. noise and emissions standards. #4 Delete kit = do you mean the AIS system? No performance gain, again an emission item, unburnt combustion chamber charge (if any) is routed to airbox to be re-burnt. Deleting the AIS saves weight, and may prevent some popping on decel; no more. #5 More power CAN be obtained by using an engine programmer to reset (or fool) the stock ECU. Again, stock the unit is set up for mileage and emissions, not peak performance. I'll let slide "rejet", I sometimes slip and say rejet on a fuel injected bike when talking fuel management because of dealing with carbs for dog's years.
You will find no shortage of help on this forum, check out some of the stickys on modifications and do all the ones you are comfortable with. All the free mods will make it run like Yamaha wishes it could have imported it. OnlyYOU can say if ANY mods "need" to be done. Compared to the CRF230L or KLX250SF the WR250R/X runs pretty good box stock, and there are several regulars on this site who have done no mods. Further mods (engine programmer, exhaust, and major airbox mods) also have previously been covered. IMHO they should be done concurrently for best results. Leave it stock until it can be done properly.
Sorry if you feel I'm being a little harsh, I'm just trying to educate you and any others who may post in the future on the best way to help US help YOU. Remember, when posting for tech advise there is no such thing as too much information.