It's a little bit hard to figure out the situation without a picture, but I think the problem is that 9x10=90 km is too far away and makes the picture too big. Try using a smaller factor or no factor at all.
I made an interception sketch of your situation using Google Sketchup as I'm not at an SH3 equipped computer right now and got an interception course of 347 true degrees.
I would also intercept with a faster speed. You don't have much speed advantage in 12 knots against 9 knots.
And btw your question is not really related to modding. It would have been better placed in SH3 forum.