Measurements (am I doing this right?)

Not sure what you're asking. But after looking at your pictures, on a couple pictures your "0" mark on your tape ruler doesn't start at the beginning of the fabric. Refer to the first imgur link, hem measurement for example?

Yes, that's adding a decent amount on some measurements alone.

Also, when measuring for instance the thigh, don't stop the measurement at the out seam, include the fabric to the right of it as well.

Go by what any given brand or store uses for measurements in their guides. When in doubt, ask the retailer for exact measurements on a specific pair in the size you want. I have done this with Blue in Green before and worked great.

Oh man, I just remembered "tape measure calibration". Anyway, the tape measure is fine, you've got the general idea correct, but on the measurements starting at the end of the tape you're removing an inch from the measurements. For example I think you were hitting 17.5 on an 18.5 measurement of the waist. Always start your measurements at zero, or just add that inch to the measurements you get starting at the end of the tape. If you're going for a somewhat modern or slim fit, that inch is going to make a world of difference.