2. It helps to think of that stage as having selected the qualities, but you pay karma for them in step 4. End of day, you have 50 karma to spend, and you can't have more than 20 additional karma by taking negative qualities.
3. Yes, specializations cost a skill point. You can only have one specialization per skill, and you can't buy expertise.
For point 2, CRB6 states "the net bonus karma" cannot exceed 20 points. Wouldn't that mean that mean you can take 6 qualities (both positive and negative) so long as you don't end up with more than 20 extra Karma?
i.e. A character could take Gearhead and Juryrigger for a total cost of 28 karma, then take Honorbound, Uncouth, Prejudiced, and Bad Rep for a total bonus of 32 karma. The
net total bonus karma is only 4.
For point 3, CRB6 state specializations and expertise both cost 5 karma each. so you would need to have at least one rank in a skill to get a specialization for that skill, and you need to be rank 5 in a skill to be able to advance a specialization to and expertise.
i.e. Your Street Sam has one rank in Piloting. He could spend 5 karma to specialize in piloting Ground Craft, but he could not increase that specialization to an expertise. Conversely, if your Street Sam had 5 ranks in Firearms, he could spend 5 karma on a specialization for Automatics, and a further 5 karma to bring that specialization up to an expertise.