I'm not very familiar with JR 50's, but I would anticipate the FMF pipe and silencer would uncork quite a bit of power. From what I know, the stock exhaust looks pretty choked up.
On the oil injection, I think you're going to need to disconnect and plug some lines, so as not to suck air in through the injection system and lean the air/fuel mix out. Simply emptying the oil tank will let air pass through. You can leave it intact, just disconnect the line from the oil tank to the pump, and plug the pump inlet and tank outlet off so that air is not going to be sucked in.
Beyond that, I'm not familiar enough with the bike to say for sure.