I understand your frustration. And as you've already learned (and for 'others' to realize), planning says a lot. And when it comes to painting, prep work is the 'hardest' part - The painting, itself, is the EASIEST. Chalk it up to a lesson learned the hard way. (And welcome to the club!!! It's NOT that exclusive. Not only am I a member, I'm the President ...)
Anyways, PRIMING / SEALING the under-layers is important. And if you're hesitant in the slightest, go ahead and put on a 2nd coat. Sure, do the ENTIRE ceiling if you're hesitant in the slightest. (And from where you've come and from what you've learned, you should be a bit gun-shy.) Oh, and DO use latex. After you're finished Priming / Sealing, plan on 2 top coats.
Now, I hope I'm not too late. FORGET the Home Center primer and paint. Go and get your YELLOW PAGES and open it up to the section labeled PAINT - RETAIL. You should see listing for Sherwin-Williams, Benjamine Moore, possibly Finneran & Haley (my personal favorite), and the like. SPend about $10+ more per gallon than you're use to and get some good paint. You have to wonder about the Home Center paints. IF they're selling it for $10-15 per gallon, and making a profit, how good can the paint be? Believe me, in my own personal opinion, the extra $$$ is $$$ well spent.
YOu know where to find 'us'. My best to ya and hope this helps.