I think the wobble mamemaster was referring to was if the wheel wasn't perfectly perpendicular to the shaft. If it wasn't, it's possible that when the wheel spins, the tab on the back of the wheel wouldn't go through the opto. Since you say yours is doing that, you'll need a systematic way to find the problem.
The mystery wheel opto on Cyclone is a unique switch in that it's the only switch in column 6 in the switch matrix. This means that the rest of the game can be working fine but if the mystery wheel isn't working, it could be any number of things.
First, isolate whether the problem is the mystery wheel board or the MPU. Remove connectors 1P8 and 1P10 from the MPU - these are the two connectors in the middle on the bottom of the board. Put the machine in switch edges test (07 in player 3 display.)
Connect a jumper wire from pin 9 on 1J10 (left-most pin on left header where you pulled the connector) to pin 7 on 1J8 (3rd pin in from the left on the right header where you pulled the connector.) This should trigger the home opto switch on the display (41.) If it does not, AND ALL OTHER SWITCHES in the game work, you have a bad column drive transistor Q47 on the MPU and it needs to be replaced. If 41 is triggered, the MPU is good and the problem is the mystery wheel board.
You should be able to manually trigger the opto with a piece of paper. Reconnect the connectors, get an 8" long piece of paper and fold it so it is stiff. You should be able to slip it behind the wheel, through the opto and trigger the switch open.
If you can't trigger the opto with a piece of paper and you are sure the opto is good, you need to check your 12v line going to the opto board. If you're not getting 12v, the opto won't work and the wheel won't spin properly.
Another way you can tell the opto isn't working is by running the mystery wheel test. As it spins, the P4 display shows an "H" on the left indicating the opto is interrupted and on the right a number that shows a count on the stepper wheel. For about half a rotation of the wheel, "H" will appear in the display, the other half it won't (the two blue 10Ks on the wheel are the dividing lines.) The number on the right should never go above 200. If you don't get an "H" for half a rotation, the number on the right can go up to 256. If it does, the opto isn't being tripped and the wheel will not work properly. If the wheel is installed properly on the shaft and the opto is working, it should index properly to stop on the appropriate values.
If you need pix of what it should look like let me know and I can snap some for you.