If handing out participation prizes is an issue in regards to time, then do what companies who put on GPs for MTG have done (not to further slam MTG ideas onto pokemon, but holistically this makes sense), and that is give every player a ticket/voucher at check-in which is good for whatever the participation prize is. They way I've seen it done in the past is while collecting deck-lists, the judges will hand out the little voucher. It is then on the player to go get the prizes whenever they feel like it.
Another time-saver is to cut the lunch break for players, especially in masters. Judges can still get a break by having multiple ones to float in-and-out via rotation. I get removing a break for juniors and seniors is an issue due to their age, but their tournaments are typically shorter thanks to less players making it less of a problem. Masters, if I remember correctly, begins at age 18; these people are old enough to be able to handle the loss of a break in order to grind through it all.
Lastly, I feel it weird to shift from Bo3 to Bo1 mid-way through the event. Either it should all be Bo3 or all be Bo1. 30 card decks could be fun, but only if Pokemon limited wasn't completely dreadful. At the very least make deck size consistent with limited, so 40. 30 cards seems a bit too small to get any sort of unity and cohesion in a deck. Those 10 extra cards, especially in this game where powerful draw is a thing, go a long way to ensuring decks play as intended more games than not.