1989 Yamaha Big Bear 350 CDI Question

[Jed]

I recently acquired a non-running 1989 Big Bear. PO told me it would need a carburetor. I tinkered with the fuel system enough to get it running and drove it around enough to ensure the drive train was working (probably 1.5 - 2 miles).  A few minutes later I attempted to start it to move it back into the garage and it wouldn't fire. Checked for spark at the plug (wire held close to block) and no spark. After getting it back into the garage and checking a few things I concluded it was likely a bad CDI box. I went on line found an aftermarket box that was advertised as compatible with an 89 Big Bear. When I installed the new box, the quad still would not run but each time I hit the started button I would get a single spark (turn key off and back on . . . hit the starter button . . . another single spark).  When I got the new box I did note it was not identical to the old one(had an extra wire in one of the connectors). The part number on the box says it's a 1YW-85540-20-00. The box I took off the quad is marked 3HN-00. Which I understand after looking at a parts diagram likely means this is a 3HN-85540-00-00 CDI box.

I reinstalled the old box and confirmed the quad has no spark with that box.

My question now is whether this new box will work on this quad, given the apparent part number discrepancy, or do I just have another issue somewhere in the ignition system?

Any insight would be much appreciated.