So I managed to solve this for myself in a very roundabout kind of way. So I
figured that I should share in case anyone else needed something like this.

filled.contour(contour, axes=F, frame.plot=F, color=terrain.colors, ylab=
"", key.title = title(main="Velocity\n(m/s)"),asp=2, key.axes = axis(4,
seq(0, 0.6, by = 0.1)), plot.axes = {
axis.mult(side=1,mult=0.005,mult.label="Width (cm)")
axis(side=2, at=x, line = -5, labels=colnames(contour)) })
mtext(side=2, line=-1.5, 'Length Along Flume (m)')

I just removed the frame.plot then manually shifted the axes and axes label
over until they lined up nicely with the edge of the actual contour plot.
Anyways, this is solved and thank you for your help.

Sam

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