My 2 cents: I've installed 4 of the side windows so far and had minimal issues. I seriously considered cutting from the outside and rather than drill holes to transfer the inner "line" I used an automatic center punch. That way the metal remains intact and won't flex or vibrate as much under cutting stress as it would with all those extra holes in it. But this method proved tedious (for me) and I decided to cut from the inside.
I made a quick template of the CRL window (using heavy wrapping paper and a soft pencil) because I didn't believe for a second that it would follow the "factory" lines and I was right. Realizing I would have to cut into the inner second layer of metal I did a trace adding about 1/8" extra on the cut line.
I used a rotary cutter (round blade mounted on a die grinder) to make the initial cuts, then used a reciprocating saw for all the rest of the cutting as I had better straight line control with it. NOTE: because recipro and jig saw use a back and forth cutting motion, it can set up wicked vibration on the sheet metal, especially if holding the saw off the surface. Therefor I used copious amounts of blade lubricant (available on line or at a real hardware store) to help alleviate the chatter and make the cutting go fast.
When I was done with the rough cut out, we held the window up from the outside and used a Sharpie to mark all the areas that needed extra relief, finishing those up and all of the edges with a rotary drum sander. This left a nice smooth surface that required minimal handwork to get rid of any left over sharp edges.
I used an oil based paint to thoroughly coat all the edges, and allowed it to dry.
Installing the window I found the screws that came with it were pretty soft, so using a brand new phillips bit was crucial, as was easing the self tapping screws a little at a time as you go around was very important; about 2 turns per screw, starting at the top and working from the top in opposite directions, left then right the left then right, etc. Took about 3 go-rounds to seat the window and have the inner clamping frame tight against the body. I also added a few screws on the corners (had to get the black pan heads from a specialty hardware store but they are available on -line)
My windows came with a thick rubber gasket installed. I used a little soapy water on it to help "lube" it into it's proper "squish". No leaks at all!
It took me about 7 hours to do the first one, then about 5 for the rest. "Slammit" told me up front it would take a day per window so I knew it would be time consuming; not have expectations relieves a lot of stress! Also talked to a pro installer who does 4 in a day but he has hard templates, and uses a sheet metal nibbler which leave very clean edges eliminating the fitting and clean up.
I can't emphasize enough the importance of masking everything off to keep metal shavings out of everywhere. New vans have a yellow wax sprayed inside the body and that stuff just holds shavings against the strongest shop vacs so cover and tape all the holes, even ones you think won't get crap in them! This is where the pros cut time as nibblers don't produce shavings and templates make the holes perfect, so no dickin' around with all that fit and clean-up
As shouldbeeasy mentions, just work slow and carefully, you'll get it.