So I'll be tuning for Speed Density, my question is:

I'll be running a maf free intake, can I go ahead and install that intake and begin the tuning process, or do I have to leave my maf hooked up, finish the tuning, and then install the new intake?

 

It depends... many tuners use MAF to calibrate the MAP sensor by having MAP air counts match MAF air counts.
I like to calibrate the injectors using MAF before removing it & converting to SD.