Trouble with New Custom Tune - Engine stalls at low RPM & Startup sounds Oddly

I have a 2006 GT Automatic and I installed a JLT CAI and uploaded a custom Tune from Bama Performance using my SCT tuner I bought from American Muscle. So now I'm ready to take a test drive. I go to turn on the engine and it when it starts up, the RPM started really low as if it was struggling to start then it shoots up to around 1000 RPM and stays like that for a while. So I pulled out of the drive way and as I approach my first stop sign, the RPM drop completely and the car stalls. WTF. I called up the Bama Team and they told me to check for any vacuum leaks and to make sure the clamps are on tight and also to check and make sure the MAF sensor is facing the right direction. In the mean time they emailed me a new custom tune to try and solve the idling problem. I got the email okay but now I'm having trouble installing the update software on my computer cause I don't use PC I use a Mac and the software is an exe. file which is only windows compatible. Does anyone know SCT has a software for Mac users? And why the heck would my car stall at low throttle? Does it just take a while for the engine to except the tune?

I had to put my stock air intake back on and convert the engine back to stock as well cause I have to work during the week and don't have time to mess with it until the weekend. Oh, and another thing, after I converted everything back to stock, the engine did the same thing for the first 5 mins or so (weird start-up and died after the first stop sign) but then went back to normal which makes me think that the engine just takes time to recognize codes or tunes. Hopefully someone has answers for me cause this kinda sucks. :shrug:
 
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Here's a tip: If you own a mac, you should prolly check ahead for compatiblity with anything that might involve a computer. They're not exactly taking the world by storm you know.;)
 
No need to panic.
The ECU has to re-learn the idle strategy whenever a different tune is loaded, or the battery is disconnected. And it can take as much as 50 miles of driving before the idle returns to normal.
 
**UPDATE**
After having issues with my custom tunes and having my car idle sporadically and stall at stop signs (automatic transmission), I can gladly say all is well. I had to wait until the weekend to actually roll up my sleeves and get to the root of the problem...Turns out I needed to update the SCT Flash device first! So while I was updating that and making sure the firmware software was up-to-date, I re-installed my JLT Cold Air intake and while I was at it, cleaned the MAF Sensor and throttle body. I had picked up a can of throttle body cleaner and MAF Sensor cleaner from my local Autozone (about $12 for both cans) earlier in the week. Before I installed the JLT I made sure the engine was fairly cooled down before I disconnected the battery. Once everything was clean and in it's place. I followed the correct procedure to allow the ECU to re-learn the idle strategy and took her out for a test drive. I gotta say the power is noticeable and the jump off the line is pretty wicked. I peeled out quite a few times so it looks like I'm gonna have to get used to my foot-to-pedal ratio all over again cause my mustang feels like a new car again.