First hydroponics grow E&F

So this is my first attempt and ebb and flow. Ive got my setup built and everything ready to start first weekend of march, (business trip delaying it a bit.)

I have a few questions so far that I havn't gotten a clear answer it. I'm growing an autoflower lowryder strain. What is the best size pot? So far running tests I'm using a 3 gallon pot filled 90% with hydroton. Pot has 4 small holes in the botton sides and one on the bottom of the pot. I can let it sit for hours and water just reaches half way up the pot if that. So Im guessing too big of a pot? So just as a test I took a box cutter and sliced a few places around the pot about half way up. I now get water about 2/3 up the pot. leaving maybe 3 in of dry at the top. Which should be good right? Is there a better pot to use? I can use net pots but would have to find out a way to cover my flood tray. Or is the pot I cut ok?

I see people talking about flooding there tray anywhere from 15mins to 1hr. It takes my pump about 7 mins to fill my tray w only one pot in it. The current set up it takes about 45 mins to drain, I started off small so I could expand. So is this 15-60 mins mean total fill time to empty? or amount of time it takes to drain once filled?

My setup is a diy with out using real EF fill and drain tubes. Mine is pvc fill line that sits about 3'' from the bottom of the fill tray. and the over flow tube is about 5.5'' hight. Since my fill tube wont drain the tray I have just a hole drilled into the bottom of the tray and the water drains into a pvc bell and into the res....Sound ok?

If I use the type of pots I have now but smaller do I need to fill the tray any higher than the holes in the bottom of the pot?

Thanks for any help that can be offered.