Clearing codes
 

Is their a specific way to clear the dash codes such as gearbox fault and etc.???

First, be aware that you can clear codes and get into a mess. It also clears the OBD monitors and it's possible (but fairly uncommon) that they won't Complete and then the car can't flag codes so you can get a car that's really hard to figure out.

For your era, both engine+gearbox are controlled by the one PCM. Any OBD tool can clear the codes or you can disconnect the battery for a couple of mins (though that also clears KAM where the learned stuff is so you force a relearn - don't do that if you still have engine faults present as it'll relearn goofy stuff).

All the other modules need a dealer-type tool such as AE (AutoEnginuity).

The plan behind OBD is that you diagnose and fix (note that part) before clearing codes. Codes self-clear when you've fixed the problem. The future OBD plan is that you will not be able to clear codes except via a fix and then self-clear because people are abusing the system all the time, with bad outcomes.