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Are the engines and transmissions compatible between 1994 models and 1998 models

I'm presuming you are asking this question as you are intending to do an engine swap. As this is not an area we get involved in, it is not something we can confirm.
However, we understand there may have been some changes around 1996. We understand the earlier cars had the B3 EGi 1.3 L (1,323 cc) Mazda engine which was mated to a 3 speed Jatco automatic transmission, while later cars may have had a 4 speed auto.
Even if the 2 engines you are comparing appear the same, there may be obstacles with attempting a swap. It is not uncommon to find mounts, ancilliary items, sumps etc to be modified during series production causing headaches when attempting a swap.
I'd suggest asking a wrecker or second hand engine supplier who may have had experience with interchanging Festiva engines.