Yes, the slipped stitches on the end of the rows are supposed to carry up the side and be bigger than the other stitches. Don't worry about them. They're perfect. They are this way for a reason - to pick up one stitch for each of these larger stitches. It's your guide.
When you pick-up the gusset stitches you should always be picking up under the 2 strands of yarn that make that large stitch. If you pick up only one strand you will have holes. If you pick up both strands it will be fine.
Also, even though a pattern calls for a certain number of stitches to be picked up, if you think it looks better or needs more, than pick up more, just be sure both sides are even. As you are doing your decreases you are decreasing back down to the number of stitches you had originally. If that takes you 2 more decrease rounds (or whatever) so be it. No biggie.
AND - a little trick to make sure that you don't have a gap between the gusset stitches and the instep stitches - make sure you pick up a stitch right in the corner right next to the instep stitches on either side. Go under 2 strands and pick-up. It makes all the difference to my socks on whether or not I have a hole there (I hate that hole there! ). Happy sock knitting.