I was talking to the guy at the trans shop and he said the gt trans is way better but I'd have to get the gt ECM should I upgrade as I swap the trans or is it not that big of a difference ?
The trans is not better, its exaclty the same, only the gear ratio is different and the HD diff which means jack.
Get yours rebuilt or find another from a junkyard, you will not be able to use a HD trans.