So I have just purchased a new transponder key and fob for 04 Evo 8 GSR. I have been going through and reading information about reprogramming them. My car has an AEM EMS V1 in it. Will this cause and issue with programming my new key and fob?

 

You don't need to program a key if you have an EMS. The EMS does not care about it.

 

Will I still be able to program the key fob to the car though?

 

Key fob is handled through the ETACS and has nothing to do with the engine management. You won't affect anything with the EMS in regards to the fob (existing ones will still work, new ones will program fine).

 

Awesome thanks for everyone's help. Exactly what I needed to know.