First let me say that your bike does not 'self adjust' for after market pipes. To do that the ECU would need some kind of feedback about your Air Fuel Ratio. I looked at the online parts diagrams for your bike and didn't see any kind of oxygen sensor in the exhaust system. Whoever told you that doesn't know what they are talking about.
On your FI light: I guess we assume that because they are 'dealer' mechanics they know what the hell they are doing but maybe they don't. Again I'm not that familiar with your bike but on other bikes of that era, like the ZX-12 downloading' the FI error codes is not rocket science but they still may be screwing it up.
First of all it doesn't require any special equipment. All you do is short a wire under the seat to ground or the bike frame and the FI light starts blinking in code such as LONG LONG LONG short short would be 32. On the ZX-12 there are actually two different diagnostic modes. One show you the current codes or the state of the bike at that instant in other words if the FI light is on while you enter the test. The other mode retrieves old codes when the light came on while you were riding then turned off before you got back home.
When the light comes on how long does it stay on?
If it were me I would splice in a length of wire to the diagnostic line and strip the other end. Then when you were riding the bike and the fi light came on you could pull it over and flip it into diagnostic mode right there by the side of the road by just holding the wire against something chrome and grounded to the frame. When you pull over don't turn off the key even if it sputters and dies at idle.
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