I only have a few changes so far but I am wondering at which point should I replace the ECU (w/ Apexi or M2) and start tuning for those changes.

Currently:
GReddy Intake
M2 (medium size equivalant) IC
HKS DP

Soon:
Cat-back sys.

I don't plan to make any other intake, eng., or exhaust changes after that until I pull the engine for rebuild. So, am I OK for now?

 

You should be fine but I still would put aftermarket ecu on it just to make sure it doesn't blow and you run at safe boost.
go with pfc.
hope it helps

 

When? Now.

I would get it before I get a cat back.

 

A lot of it depends on your plans for the car. If you plan on keeping the stock ports, turbos, and fuel setup then you don't need a PFC. If you plan on changing one or more of those, then you'll need a tuneable ECU like the PFC or the AEM EMS.

I'd say get some type of engine management now, whatever you decide to do.