What type of cabinets did you order? Are they the classic face frame setup or the European style with no face frame? Is this gap along the front side of the base cabinet or at the back?
Cabinet style makes a difference because each box is built differently. The euro style won't have any additional material to scribe. In that case, the gap is what it is. You can order scribe molding to cover it, or favor the decorative end panel closer to the wall which will likely hide the gap in shadow and make it unnoticeable. Without seeing it, it's tough to help.
I always install straight, plumb, and square. Just because the rough framing is effed up, doesn't mean my cabinets are going to be. Sometimes you can dig out some drywall if absolutely necessary. Find your highest point and set your elevations based on that. Find your furthest wall projection and base your face location on that. I like to set the cab elevations and fasten them together before fastening to the wall. Be sure to get lots of clamps, they come in real handy keeping panels nice and tight. I use 2 or 3 points along the front, and 1 point at the top rear corner. A 72" level or longer helps to line up and maintain a straight face.
There are tons of tips, tricks, installation procedures that go into a professional install. Lots of years learning this stuff, and it's impossible to relay it all in a forum post. Pics certainly help a lot in visualizing what it is you are asking.
A 23 guage pin nailer comes in handy for face nailing panels and trim. Leaves a minimal hole that can be easily filled with the supplied color matched hole filler (order the touch up kit!). 18 guage brads are reasonably invisible when filled as well.
Hope this helps a little!