Curtis,
I'm more of a player than a builder, but I'd be glad to put my 2 cents in.
I have a Les Paul DC Standard with a serial number saying it was made in February of 1998. I bought it in early 1999, and it's been my main guitar ever since. I LOVE this guitar, it's the best one I've ever had as far as playability and tone.
I'm no expert on building, and others in this forum are certainly way more qualified than me to be helping with this, but it seems to me that the answers to your questions are a matter of taste, depending on the setup. These measurements change during setup, when you're adjusting the truss rod for neck relief, etc. The strings can be raised and lowered to taste to fit your playing style, as long as the notes don't buzz out, and the intonation is correct. With that being said, I took some measurements on my LP DC to give you a ballpark figure to work with on your drawing.
1. The string height between fretboard and string is slightly different for each string, and different depending what part of the fretboard you're measuring (closer to the nut, or closer to the bridge). Especially if your talking thousandths of an inch. To make this easy, I measured the lowest-pitch E string, on the fretboard between the 6th and 7th fret, at a height of just less than 3/32. This measurement was from the top of the fretboard to the bottom of the string, and I'm using a small metal straight edge ruler, with 1/32 as it's smallest increment. To do it correctly to thousandths, feeler guages should probably be used, but this ruler is all I have right now. I would say 3/32 is good enough on your drawing, afterall, if you drink alot of coffee like me, you could NEVER draw a line that would be that accurate anyway! lol Wait...oh yeah, you're using CAD... guess I'm from the old school when it comes to drawing!
2. The distance between my guitar top and the string at the bridge, using the same string as above, is more like 5/8". When I say bridge, I mean where the string crosses the saddle. Also, my guitar is a carved top. The body carving directly under the bridge seems to follow the radius of the saddles.
I hope this helps. As I said earlier, I'm no expert on building, and I hope I understood your questions correctly. I do have one of these incredible guitars and at least can take some measurements of it. This should help get you close, anyway.
Best of luck!
Lance