I am thinking that you might want to take pictures and post a full listing of how you connected each harness.
I am hoping that you recognized that the wire color-code of the pigtails does not match that of Crystalyte - so if you used RED for +5V, BLK for GND, and Yellow for signal (etc) you will have to either pop out the pins and reconfigure them or change the throttle pins etc.
I have posted this before - but here is how I wire mine.
I chose this wiring order for a reason - if you plug any two connectors together you will not get short circuits etc.
Methods #6
Max Voltage: 100V
Min Voltage: _____
Shunt: 332uOhms
Regulator settings
1.8 || 1.8 || 1.8
input 70v~ 105v
1.5 || 1.5 || 1.5
input 60v~ 86v
1.8 || 1.8 || 0.68
input 50v~64v
1.5 || 1.5 || 0.68
input 30v~54v
Hall – 6P
RED +5V
YEL GND
GRN A
BRN B
GRY C
BLK N/C
Throttle – 3S
RED THR
YEL GND
BLK +5V
Brake – 3P
RED BRK
YEL GND
BLK +5V
CA – 6S short
BLK VBAT
GRY GND
BRN SHUNT-
GRN SHUNT+
YEL SPEED
RED THR_INH
NOTE: There are two versions of the 6-pin connectors: If your connector has a BLUE wire on it, just follow the linear order shown.
The reason I used 6 pin connectors for the Hall was because the 5 pin are not readily available.
The 4 pin connector was intended to be used as the USB programming harness but it does not really matter.
Be sure not to "hard wire" the USB cable directly to the controller because A) you will have 5' of USB cable dangling and B) you will have to add a button to get it to program. I just "plug" my 4-pin connectors together when I want to flash the board. Never had a corrupted flash.
Anyhow - try to take some time and post some pictures.
Post up your connections in detail and we can look them over.
-methods
P.S> Thanks to those who are helping field questions. Group effort

I have been super busy lately with my next project.