Guthrie Govan wrote down his 10 top improvisation tips for Guitar-Bass.net. Here's the last one of his list: "Apply theory with musicality":
There’s no harm in learning as many scales and arpeggios as possible – quite the opposite, in fact – but some players seem to expect scales to solve problems that in fact they were never designed to solve. You use scales when you improvise in much the same way that you would use the alphabet when writing a poem – an essential part of the process though it may be, the alphabet alone is obviously not enough!
As soon as you’ve learned the shape (and sound) of any given scale, try jumbling the notes up in as many ways as possible – and be wary of traps such as always starting from the lowest note! It can be helpful to fire up an appropriate backing track and play the scale at an excruciatingly slow speed, counter-intuitive though this may feel, as doing so will help you to develop some sense of the different ‘colour’ and mood evoked by each component note. You can use the component notes of a scale much more musically if you’re aware of the unique character that each one possesses, relative to the harmonic context.
He is on tour with The Aristocrats, promoting their latest album Tres Caballeros.
HCTF review of Tres Caballeros.