1st. when transplanting, you want the size of the pot to reflect the time that the plant will be spending in it. 3 months equals a 3 gallon pot. 6 months = 5-7 gallon pot. and so on and so on.
2nd. the reason for "stripping" the bottom of your clones is to not waste energy on growth that will not produce a high yield, rather, divert the energy to the canopy of the plant, where most of the magic is happening. Also, cutting the larger fan leaves in half (Hamburger Style) will trigger the plant to produce a larger root mass. As far as planting deeper, it's a matter of preference and situation. Clones don't grow taproots, so they tend to grow wide root masses as opposed to growing deep down.
Hope this helped