The idea with this is to progressively overload AND ratchet up caloric intake synergisticly. With this in mind we set the programming up to be relatively easy up front to allow for some momentum to be generated. That is one element of the program. Another element of the program is simply getting stronger seems to be the best correlate with increasing muscle gain, especially if nutritional status is adequate. With this in mind the alternating mesocycles involve enough work in the hypertrophy phase to stimulate growth, and enough neural work in the strength cycles to improve recruitment and come back stronger on the next hypertrophy go-around.
Now in your case it may be smart to shift to 60% of your front/back squat as necessary. As the Late JV Askem wrote "Nothing is written in stone!"
In fact here is a great 5x5 article from JV:
That is phenomenal piece with simple progressions that are really the key to get from intermediate towards advanced with regards to strength and muscle gain.
If you notice in the 5x5 piecee a light weight(60%RM), moved quickly, can and will provide a nice growth stimulus.
So, as far as what to do...what is your current 1RM front squat? If it is significantly higher than your clean (assuming good form, depth etc) then by all means, use that for your 60% guide. Then make that weight move fast, progress as per the Mass Gain guide, eat like crazy and let us know how things are progressing.