Deceleration Settings??
 

I am running a MSPNP in my 97 miata and have roughly tuned the PNP maps for my setup. I recently replaced the 390cc injectors that I was running with 550cc injectors. After a lot of screwing around with acceleration enrichment numbers, I have it pretty much dialed in. I am running into some smoothness issues while decelerating. When I lift part way off the throttle, I get a burbling from the exhaust and the AFRs change rapidly back and forth between about 11:1 and 15:1 and the engine surges very mildly. If I lift completely then the over run fuel cut takes over and it is smooth again.

Any suggestions on which settings I need to change to smooth things out??

Sounds like you've got your overrun settings funky. If you've got the kpa point set too high or the TPS point set too high it'll do what you're describing. Observe your overrun in a data log and set it to 1kpa above the lowest number you see. thats what i've done.