Hey Yonder
Sounds like poor design if the gear leaked at zips and pockets. If you can see, are the seams taped? If not, that'll be why it leaked. What is the waterproof bit made of? Is it some kind of membrane like Goretex (or even the real deal)? If so the garment must meet their standards so you should have some come-back if it doesn't.
As for the boots - all membrane boots will eventually crack the membrane leading to leaking. The membrane is a thin layer of (usually) some kind of ptfe, which after much flexing (particularly near the toes) will split, rendering your boots useless in the wet. Another possibility is the old problem with that huge hole at the top - if the bottom of your jeans got wet, it's also possible the water ran down into your boots! One other fantastic thing about goretex - it's equally good at keeping water IN...
If your gear is under warranty, take it back. If not, get some really good stuff next time - I use Rukka and it's never let me down.
ps - like the unixbeard tag. I'm not going to stalk you, but being a fellow geek I'll read your blog

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Andy