You need to first find out if the problem is with the system that the light is checking, or is it with the light circuit itself.

What does your manual state causes the light to come on? In other words, what system does it say is malfunctioning?

It is possible that lowering the t-case, thus placing a "tilt" on the entire drivetrain (engine, transmission, and t-case) put some kind of strain on the drivetrain, thus making the malfunction light come on. That is the more serious posssibility. Most people who lower their t-case are not aware that doing so can change the oiling characteristics of major components, some models more than others.

On the other hand, it is also possible that lowering the transfer case caused something in the malfunction light circuitry to go awry -- like a wire or tubing or linkage being stretched or rubbing against something because the t-case is now in a lower position than stock. I would crawl under the vehicle and really check out this possibility before doing anything else.

A third possibility, which should not be overlooked, is that the malfunction light coming on isn't related to the lowering of the t-case --- whatever is turning the light on may have just coincidentially malfunctioned at the same time the t-case was lowered. I'm not a big believer in coincidence, so I would investigate this possibility last -- but it could happen.