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As each dealership probably would quote you a different price, there's no way to tell without calling.
That said, what makes you think it's the injectors? And (if they are defective) what makes you think replacing them will fix the issue that caused them to go bad in the first place?
I'm going to ballpark $2-5k for engine repairs through the dealer to fix your problem - unless they won't even touch a modified engine bc they can't warranty their work, in which case they would probably say return it to stock, and then they can look in to it, or suggest you buy a whole new engine.
From your post it's impossible to say really, but I'd go through the shop that installed your FI system (supercharger or turbo?) and see what they say. Though if they messed up the job, they might not be the best shop to have working on your car.
Good luck.
Edit: my other car has an aftermarket supercharger added, though it was arranged through the dealer but sent to Dinan for installation, it's still aftermarket. Whenever I have work done it costs extra bc they have to remove the supercharger to get to the valve covers, etc. And then of course they have to re-install it when they're done. No fun. Ok, the supercharged V8 is fun, the maintenance costs - not so much fun.
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