Offset left to right of the pinion is just fine, so long as the pinion centerline is parallel to the transmission centerline and they should be already unless your engine is installed somewhat sideways or your axle is askew.
Just like it is OK to have the pinion lower than the transmission, again so long as they have parallel centerlines.
The compound angle calculations come in when you figure if you're in the safe operating range for the universal joint. It's easy in one plane, can be measured with a simple angle meter, but throw in another axis and you need to do the calculations to find the total angle of the u-joint.
Skim through the driveline tech tip again
http://www.stovebolt.com/techtips/driveline/setup/index.html and look at page 9 of the installation manual.
"When you have a compound angle, you have to calculate the "True Universal Joint Operating Angle" of each universal joint. It is
the True Universal Joint Operating Angle that must meet the three rules shown on page 5."
Grigg
