Hi UG - Merry X-mas buddy!
Well, if your tap water has PPM's that low, you may not need an RO system at all. Mine is around 300ppm out of the tap last time I checked, so I like the RO system. Unless I'm missing something, you might just want to let your tap water off-gas for a day or so, and skip the filter. Sounds like you've got great water to begin with, unless you need to filter out chloramines or something.
As far as question 1, that's exactly right and normal. The black line (drain line) should be coming out much faster than the blue line. Unfortunately, RO filters aren't super efficient that way, although I think some of the newer ones are more so...
On question 2, unless the water or the containers are contaminated with soap or similar, it's probably just oxygen bubbles or something. I've never noticed any unusual bubbles or anything with my water, but air bubbles from pouring could be part of it I suppose. Sometimes air bubbles gather on the sides of the container, but are just normal from pouring.
You can get calibration solution for your PPM meter, that should help you understand whether it's reading correctly. Local hydroponics stores should have it - or online, etc. Maybe you have that already, but in case you aren't sure your meter is working correctly.
Hope your holidays are fantastic brother!