I have wiseco 11:1 piston, full port and polish, titanium springs and retainers, stainless 1mm oversized back cut valves, 254 degree lift cams (intake and exhaust) and the Fuji Racing IRTB kit with 99 fuel injectors. The AEM stand alone is a direct plug in to the factory ECU harness.
The tuner has everything hooked up but they are talking about having to modify my kit with welding and such which isn't required but it sounds like they have never worked on a car without a turbo before. They reassured me they could do it and then have spent two days trying to figure out how the ITB kit works. They are asking me to come by in the morning to sit down with them and discuss my options and my "bill" that is supposedly accumulating when they already gave me a set price up front.
I'm just trying to find an honest and reliable tuner to set up my fuel map and get everything dial in without trying to sell me modifications. I installed the ECU once myself and almost got it to work but I don't know enough about fuel mapping to tune it myself. The throttle bodies I installed myself and had no problems with them really.
Sorry to be blunt, but "making it run in the first place" is "repair" or "installation".
"Tuning" is when it runs already and you are optimizing.
If you did not deliver the car in a running condition, you are at their mercy. You basically delivered them something which you actually know more about than they. Good luck finding anybody who has experience with that specific throttle setup and that specific ECU, all in a non-stock motor. Nothing is plug n' play when you are dealing with this sort of thing, since rarely does the same combo exist in more than one person's car. And then, you'd have to find the same installer that built that first car to gain the benefit of that experience. So you are left asking someone else to finish your install...and then "tune". The former requires you to pay for their time to learn about Fuji ITB's, and perhaps even learning the AEM when applied to a Miata (all applications are somewhat different), especially when dealing with ITB's.
Just because something physically plugs into a harness, does not mean that the internal tables and functionality are setup to actually run a non-stock application. Having done it myself, throttle body setups take some very clever ECU programming to make them work well. You will have to solve problems like: 1) How to get a non-pulsing MAP signal while maintaining good vacuum supply for brakes, 2) How to deal with high-overlap cams at the same time as lousy low-throttle MAP signals (this is TPS/MAP blend in TEC-speak), 3) How to physically synchronize the throttle plate idle screws, 4) Where does my IAT come from now that I don't have an airbox? And plenty more...
It sounds to me like you totally have underestimated what it takes to make this setup work, and they perhaps overestimated their capabilities to do so.
I know people that could make this work for you. But you will not like the price tag.