Those controllers work well. No PAS input, so if your bike had that; no more. The throttle with cruise control is better better than PAS, IMO.
From the "Manual" and the circuit board, you should be able to figure out most of the wire except for 2 or 3.
The Red and Black thick wires go to the battery. There are usually 2 smaller red wires also connected to Battery +. One for the alarm (probably not used) the other so you can put a switch between the battery and Vcc (controller power) and turn the controller off and and on. Vcc is labled on most boards always toward the back opposite side where mosfets live.
Phase wire are the 3 thick wires Y G B.
The 5 hall wires are R Blk Y G B and they will be in a row on the circuit board usually marked 5v, U, V, W, GND
All black wires and 1 of the white wires go to GND. Double check with a ohm meter/continuity tester. The throttle, 3speed, low brakes, cruise, reversing, learning and power to the anti theft all have 2 or 3 wires and one of them is ground. If you mix up the blacks (and the learning ground white) it doesn't matter.
The orange is cruise (current throttle position is locked until you touch, brake, throttle, 3 spd.
The throttle (called transfer line) has a red(4.3v), green and black all together
Any wires connected to the same pad as the Yellow Phase wire are for the alarm (you probably won't use).
The only small yellow is for brake high (you probably won't use)
The brown is for 3spd switch low (when connected to ground)
That should leave only 2 white wires and 2 blue wires to figure out.
If one of the blues is next to the brown on the board, it's usually the high of the 3 spd switch. Sometimes it's far away from the brown. The other blue is the alarm sense. You can test. If one of the blues changes the speed of the bike when connected to ground that's 3spd high.
One of the unkown whites is brake low (turns off throttle when connected to ground) the other is the learning wire that isn't connected to ground. You can safely test those.
Never cut off connectors without ID's, Just a loose piece of shrink tube around any wires that had the same connector is usually
enough to figure out everything.
Be sure to cap (hot glue?) the ends of unused wires so they don't touch something bad.
Good Luck