Well I am not sure why one is larger and one is smaller - unless it makes it so that you put the correct wire on the proper terminal.

One is the power supply - it is the red and yellow wire.  The other wire is the one from the ignitor assembly and it is black and yellow.

One thing you could do is to connect a small test light to the yellow and orange wire, and run the other end to a ground.  This will allow the light to shine whenever electricty is going to the coil.  If you are riding and the bike stops at the same time the light goes out - then you know it is something in the Safety Circuit that is killing the engine.....most likely a side stand switch or broke wire somewhere.  If the light stays on when the bike stops....then it could be something in the ignitor, coil, spark plug... or it could be a fuel flow problem.  Generally problems with electricity fail almost instantly - while fuel problems are generally more gradual.

I have the tank off my bike right now, and I can look and/or take a photo tonight when I am home.

Here's a picture of the coil on my 2007 S40.
The extra green wire on the ignitor terminal
goes to my tachometer.

Todd:  Your camera is better than mine.

Steddy:  Pay no attention to Todd's black wire....you won't have one.  My bike is a 2004 and the top wire is yellow and black, the bottom wire is orange and white.

Steddy:
Sorry, I forgot to mention the black wire on the "fixing post".
That is the ground wire for my tachometer.
The fixing post was the handiest place to connect it.

Update - I've just been looking at the wiring diagrams and if we look at the coil ( C ) as connections 1 and 2  and the igniter ( I ) as 12345 and 6.   On the 1987-1994 diag. ( mine ) the  black and yellow ( BY ) wire goes from conn. 2 on the coil to conn. 5 on the igniter and the Orange and yellow wire ( OY ) goes from conn. 1 on the coil to conn. 3 on igniter - now then, the 1995 diag.has the BY from 2C to 4I and the OY 1C to 3I and to make matters even more murky the 1996 to 2003 wiring diag. has BY from 1C to 4I  OY going from 2C to 3I. The wiring diag. for 2004 is similar to 96-03 apart from the C has moved to the other side of the I - discuss    :'(.

quick modify I'll try and make it a bit clearer

87-94 ( my bike ) B/Y wire 2C to 5I
                         O/Y wire 1C to 3I

1995                   B/Y wire 2C to 4I
                         O/Y wire 1C to 3I

96-03                 B/Y wire 1C to 4I
                        O/Y wire 2C to 3I

2004 same as 96-03 apart from in the diagram the coil has moved to the other side of the igniter which probably has no relevance   and just as a theory couldnt someone produce a 3D wiring diagram so that you can picture it a bit more clearly

Steddy58 wrote on 01/04/14 at 16:13:42:


which, now I study the posts in the cold light of day after a good nights sleep, is exactly what Dave said