What are you doing a Pluto working for? Also what runes are you using, are you vibrating Yama or something?
For your first question, Pluto and Neptune and any planet influence especially the outer ones which are odd, violent and/or benign, are made functional in the human soul because of the Moon which is the Cardinal planetary force for those 2 more intensive planetary energies. The Moon is the juggler between the storm of Scorpio and the nebula of Pisces. The Moon is thusly very important for us, which is why it rules the pineal gland and whole 6th chakra whereas the other 2 only rule parts of it and other chakras irregularly. The Moon is the closest planetary body and is core to the soul so for sure, the state of the Moon is more important than the state of Pluto and others. For a focused, spiritual mind the Moon really is all you need as it already works with those other polarities in of itself. The Sun and Solar plexus functions in combination with the 6th chakra, with time, are also what cultivate personal intensity if that's the side of Pluto you are after.
For your second question, I had the same problem once. Cleaning your aura is like brushing your teeth or showering, its supposed to be effortless after you grow into Zevism. You don't need outer help like a kid's parents who has to show him how to brush his teeth, when you have done it for a while. The outer condition like the Gods and the knowledge that comes to you and everything, helps initially and sets the tone for your future with cleaning, but ultimately that's already been and done. You're not doing the Mer Ka Ba or anything, just brushing your teeth. If you're cleaning routine consisted of deep cleaning then you should definitely adhere to good timing, so that would be like a doctor's appointment or something :D .
You don't have to worry about the timing for stuff you are mostly proficient at already or is fundamental. If you are meditating and doing visualisations of white-gold light, as well as Ritual's, there's no way your aura is going to be at fault so learn to let go and chill. If you don't already, cleaning your aura during masturbation is something which also builds on top of whatever other cleaning you do which you say you are unsure of, the energy cleaning sensation comes much easier during it, so you will have more security that you are in tip top condition there.
Skipping a day is bad yes, and it screws up the working particularly if you sleep in between it, which obviously you would have to if you didn't want to continue the working groggy the next day. You should just restart it. Patience is a virtue in Zevism like Mageson says with the Slothzin meme. If you are going after Pluto with one of those bullshit squares though, then sayonara boy, that's the worst opposite of patience- deathly impatience, accidents and etc. If you are using the runes/other mantras and are just calling it a 'Pluto working' then good luck.