So I got my MV-1A motherboard and the Neo Geo 150 in 1.
Problem is when I hook my Jamma Harness up, I get picture… But no controls.
I do notice the original PCB had two connectors… now the new one only has a slot for one 
Lol, the controls are dealt with via the JAMMA interface. Those two connectors are for external controllers.
Theres what I am talking about… err
It wont even let me select hardware setup
Probably some sort of grounding issue. Does your JAMMA harness have all eight ground wires and are they all connected together? Check ground continuity with a multimeter…
The other harness is not a part of the JAMMA standard, but looks to be a CPS2/3 proprietary kick harness which is not used with any other platforms. Your NeoGeo motherboard expects button 4 to be connected to pins 25 and c on the JAMMA harness.
Yeah, you need to rewire a few things so that it ends up like this:
http://www.hardmvs.com/manuals/Jamma2NeoGeo4SlotPinout.pdf
Right now you have three of your buttons connected to the Jamma harness (Should be punches) and three connected to your Kick Harness. (The white plug)
You could go about it in a few ways. The easiest might be to get a Jamma to Neo-Geo converter: Adapters - NeoGeo MVS to JAMMA Inline Adapter - JAMMABOARDS.COM - JAMMA Coin-Op Arcade Game Parts - NeoGeo MVS to JAMMA Inline Adapter
And then get a DPDT switch and route whether you want your “D” to be going to the Jamma harness or your Kick Harness.
-Jeremy
ah I see. Thank you sir!
No! Those adapters are for multi-slot MVS boards. Single-slot boards are already JAMMA compatible, the only addition being the fourth button (which goes on normally unused pins so no potential for conflicts with strict JAMMA). Your cabinet may or may not be wired up with button four (and potentially five) on the JAMMA harness already, but if not it is quite easily done and no harm at all in having it wired to both the kick harness and JAMMA simultaneously.
First I’d look at the dip switches on the MVS motherboard and make sure they’re all set to 0/off. Then boot up the game, and try switching #1 into position 1/on and see if it takes you into the test menu. If not, check continuity between all grounds with a multimeter as already mentioned. Also check voltages and adjust when needed so that they measure +5.1 VDC and +12 VDC respectively when under load. If you have no idea what I am talking about, find someone knowledgable who is local to you and have them help.