Lets see if I can help - I too have a 96 GTS and have experienced this issue - took me about a year to figure it out - what can I say, us folks from New Zealand are a bit slow.
Note:I did not experience this 'missing' problem until I started run open track events.
There are two things happening with the car . First, you mention this only occurs when the car is hot - if you are getting up into the red on your temp guage the following will happen:
The computer is designed to dump extra fuel into the motor, when it exceeds a certain temp, to cool it off - when the computer does this you will notice three things.
1. engine miss
2. engine warning light will come on and stay on
3. the back of the car will turn black (from the motor running excessively rich) motor will continue to run rich until you disconnect the positive battery terminal under the hood and recycle the computer.
Second - under hard braking the engine ***** oil from the drivers side valve cover, through the vent tube and into the air box. Eventually it will **** enough oil in that the left filter becomes quite clogged. This oil also goes through the motor and if enough of it goes through this will cause a misfire, and could, but not always, have the engine warning light come on. You will also notice the car will not pull as strong as it is down on power ( not able to breathe).
A few things to look at in addition to the above
1. Confirm the battery terminal are tight - a loose terminal will cause a low voltage situation and the symptom is - engine misfire and engine warning light will come on.
2. Have the Viper tech remove all electrical grounds, clean and re-install - this can cause the same symptoms as in 1. above.
I have found the oil in the airbox to be the biggest cause of the misfire - I'm installing a Puke bottle on the car to collect the oil before it gets into the airbox.
At one event, when the ambiant air temp was 105 degrees my car got very hot and I experienced the 'running [******] rich' issue - this was scary - I mean the back of the car was oily black from the excess fuel and the coolant overflow creating a oily mess.
Prior to my last track event we discovered a loose battery terminal so fixed that and checked all the grounds.
I then did the event and had no misfire problems until the second to last session on the Sunday - all I did was look under the car and the oil was dripping out of the air box water drains - nice little puddle on the ground - pulled the air filters and left side was clogged with oil - cleaned them - reinstalled - power back to normal and no misfire.
In my humble opinion, you are experiencing the "oil in the air filter problem" Hope this helps - email me if you need additional help
Gavin