I enjoyed this one - it's not really a 'cold solve', because you can just view the missing letters as a logical exercise in grid filling and get a long way. I think the easiest way in (certainly the one that worked for me) was to get the thematic word from the clues that have their definition shifted.
I don't have a problem with a preamble that only makes complete sense as you make more progress, but I think this one could be a tad clearer in places. Crucially, does the instruction arising from the first application of the sequence apply to those selected cells - i.e. does 'rest of the grid' mean all cells that aren't part of the 'whole definition'? That's the interpretation I'm going for, but I'd be interested in hearing what others think.