89? quad runner 250 2x4 weird spark

Looking at color coding diagram from Suzuki, the important ones there that I can identify are:

B = Main line to Ignition coil
B/Y = Engine stop switch.
B/R = Main line from Magneto (ignition charge)
Bl = Pickup Coil (ignition trigger) (blue)
B/W = Ground

I can't imagine what the 6th line would be for on a 6 wire system.

I'm currently looking for a complete diagram of the wiring for my 1990 LT-4WD. So I'm sure I'll be able to identify what everything does pretty soon.

Not even going to guess what these are until I get a diagram.
W/L
L
G

ok, so looking at the two wiring diagrams, I'm pretty sure this is how the CDI's are wired.

1988, 1989
W/L Ignition Coil
L Goes to Mag (trigger)
B Goes to Mag (trigger common)
G Goes to Mag G/W (probably charge common)
B/R Goes to Mag B/W (Charge)
B/Y Ignition Switch
B/W Ground

note:
The charge and trigger circuits are isolated A/C circuits in this case. So the L and B lines can actually be put on backwards and it should still work....UNLESS One or the other is grounded inside the Mag. Same with the G and B/R. I wouldn't do it, but in theory it is possible.

It would be good to know if either of the wires are grounded inside the Mag. If, for example, G and B are both grounded, you can use a 1990 CDI and just ignore those wires.

1990-1998

G Goes to Mag, probably Trigger
B/L Goes to Mag, probably Charge
W/L Ignition coil
O Engine Switch
B/W Ground

In the 1990-1998 models they went back to engine ground for all circuits.

Here's what I have under the cover it appears some gears are missing maybe a shift fork I dont know

Yes, it has a fuel pump. Vacuum operated.

Here's the pictures of the transmission.

Joe,
1, clean a area to tear the carb apart so IF you drop a small part you can find it.
2, Remove ALL the jets, under the main jet is a second jet, It pushes up into the
throat of the carb to remove and to reinstall use a pair of needle nose to guide in
from the top bore of the slide.
3, When you remove the brass body of the needle and seat there should be a small
thimble like screen on it. Remove it and clean it and reinstall it. It did not come in my kit and it may not in yours.
4, Soak the body and blow out making sure all passages are clear and assemble.
A kit would be wise to use , but you can get by just cleaning the carb if you use care not to damage its o rings an molded gaskets. and the needle and seat.
A cheap way to soak your carb, below link... 64 oz cost me 3 bucks at the dollar store
Worked good for me I used a gallon jug cut the top out added 64 oz and it cover the whole carb body. Soaked mine 24 hours at 12 hrs or so pulled it out brushed it hosed it off and in the juice.

http://www.suzukiatvforums.com/forums/repair-maintenance/2706-home-brewed-carb-cleaning.html