Hey Guy's,
I'm on the fence about either getting MS3x (with diyautotune's ms3x wiring harness) or a MSPNPPro.

I have some automotive electrical experience - I'd say moderate

I have a 99' miata and I'm concerned with 3 things before I decide which route to take!
1) Alternator Control. I want some clarification. DIYautotune support say's both MS3x and PNPPro will run a 99' alternator. BUT I read on these forums that this isn't always the case. Am I not to be concerned? I see people buying and installing the westfieldmx5 alternator pcb. With that said, what do I have to do within tuner studio to make sure my stock 99' alternator will work and charge fine? I haven't seen many alternator tutorials on youtube in regards to tuner studio.
2) Factory A/C. I want to keep it - is there anything I need to wire up? Does the MS3x come with a more in depth instruction manual and diagrams than those offered online? As far as I know (I'm a newbie) all I need to do is go into tuner studio and adjust the idle-up in AC settings.
3) Any crazy road blocks - user experiences?
4) Is it a good idea to keep a battery tender charging the battery while working with tuner studio in the ACC position? Or ?

Please be kind - I'm new and eager to learn and get this right. I'm going to make a purchase this weekend. Goal is to get my 99' stock miata up and running on megasquirt using a base map and autotune (no I can't afford a dynotune). I'm determined to learn and want to do another megasquirt one day on a future build as well. I have a strong passion for miata's and plan to keep mine as long as possible!

With that said, are there any road blocks you think I'll run into? Thanks in advance