Dave,
I have the same motor (except its got a giant hole in the crankcase...) and I used a generic throttle cable from BMI Kart Supply. I think its off one of those dune buggy type karts. The part number is 03185 (48" Throttle / brake cable). it had the correct barrel to fit stock Yamaha F.I. unit.
At the pedal end I made a aluminum swivel block with a set screw to hold the cable. I also backed it up with another cable-thru clamp thing. I never had a problem with it. I had to cut about 3" off the end of the cable jacket (I use a dremel like its a pipe cutter, go slowly around) and attach the yamaha threaded body with nuts fitting to whatever mount you have (say on the upper part of the motor plate).
You can also buy whatever cable parts your heart desires from Flanders Cycle cable supply (
http://www.flandersco.com/FlanCableSearch.html). They have everything including tool to make them. I once had a talented guy (not me) zap a barrel end on with a tig welder for a custom bike creation. You just got to get creative. I think Motion Pro will also make you a custom cable, but last time I checked on a bike creation I had going they were very pricey...
Also, to keep the end of the cable from fraying, you can buy those metal ends that always fall off, or put on a latex / nitrile disposable glove, put some good superglue inbetween your thumb and index finger, and wet down / stroke the last 1/2" of the cable until the glue just starts to set. This always keeps cables from fraying for me.
What Dad said about finding a good independent (not Yamaha big box store) is spot on. That should get most if not all the way their as well.