Leave it in!
I've got the 97 model challenger and bought it used. It still has the injection tank and since I bought it, I've worked on quite a few things to bring it back up to snuff. Mostly, the sycro on the carbs, rebuilt the jet pump and re-worked some of the electricals (DESS).....now that can be a pain!....
What I'm wondering is, from what I've read in my manual, the oil system also is supplied by a larger hose to the bottom of the Rotax engine, for lubrication. The oil injection pump to the carbs for mixing in the gas is attached to the forward part of the engine where the magneto is. From there, there's two small (1/8') tubes that attach to the bottom of the carbs intake, just behind the throttle plate and if the carbs aren't syncro'd with the injection system, your in for trouble. The Sea Doo manual I have describes this in pretty good detail, in lamens terms, with pictures, that it doesn't seem to hard to repair yourself.
I've never been one to trust the work of others........call me cheap, but it just seems that after something I own goes to the shop, the problems never end................I say, keep the injection tank and buy the shop manual for about 10 bucks and do a little research yourself. One chapter explains the importance of using either the preferred injection oil, which is a synthetic blend of low ash oil....it MUST NOT be NMMA type ashless oil!...this will tear up your engine....or you can use the standard blend of low ash oil. Quicksilver synthetic from walmart is labeled for the Sea doo also. But you can't mix them and if you bought the boat not knowing what was in it and you put the other type in, that could be a root cause to your problem....
P.S....the information above was from research I already did because I wasn't sure what type of oil to put in the tank after I purchased it from the last owner........I love my challenger, so I hope you get yours running and can go out and have a blast!........there a great handling boat!