On page 58 point of the manual it basically states that you can place an applied dominant before a vi, IV, ii and V to make the progression slightly chromatic. I can see that to be the case for vi, ii and V but for the IV the V of it is actually the tonic so there are no altered notes. Is this right, or am I missing something?
It is important to separate in your mind function from actual notes in the chord. While the I chord and the V/IV have the same notes, the function is different. To clarify the function as an applied dominant, I would suggest adding the minor 7th in the chord.
I – V7/IV – IV is a perfectly acceptable progression progression.
In fact, a very common progression is a pedal on tonic, and the progression I – V7/IV – IV – V7 – I. It even has a name, called “the Quiescenza”.