My check guages light stays comes on and stays on even when all my guages read normal. What can be my issue? Please help

Tough to say w/o knowing what you drive.

Please put your year, model and current mileage in your signature.

If you are thinking about modding I could make a good case about how this happened to me and upon modding further things were magically fixed

1996 Bonneville SE 132k miles

LOLOL!!! r u low on gas?LOLOL!!!

Check gauges should be telling you to check something that is on the gauge cluster.

You have temp, oil pressure, fuel and voltage.

Of those..which ones are redundant or items the computer can see to alert you. (Assuming the cluster isn't doing it on it'* own and w/o FSM'* in front of me..I'm guessing)

Temp: we have dual temp sensors built into one package. PCM gets one output the cluster gets the other.
Fuel: I don't remember how this works..but in 97 it goes through the pcm.
Oil: Will alert you if the pcm thinks the pressure is in the red.

I have fuel and everything, my temp reads below 200 and the oil pressure is good. How can I troubleshoot this issue

As I stated in another thread I changed the motor, the motor that is in it now has a smaller alternator than the one 140amp that came on the original. Would that have anything to do with it?

Shouldn't, the voltage is read in volts and the difference in alternators is amps.

My thought is you may need a scanner to look at the data the pcm sees to understand what it is noticing as out of whack. Although I can't confirm that theory w/o an FSM and I don't have those here.

Hit up the local auto zone and have em run a diagnostic.

I tried that, they said they can only check it if it says "Check Engine"