So, I recently went through the effort of adjusting my action and intonation with a new string set, laying the Stick down while making the adjustments. After getting it all just right, I put it on, only to find that in playing position everything is different. The strings are too low and buzzing and the intonation is off. Any advice on set up methods?

Should I have to put the instrument on and take it off for adjustments? This also brings up the question of the board's straightness in different positions. Does this mean that if I get the board straight while laying down, if I pick it up the board will tilt back?

I've received two bits of information, and you can try both. I was told once by Greg that I ought to make adjustments to setup and intonation via playing position, which makes sense.
Then at Free Hands Academy, during his setup class, Emmett said that he makes adjustments with the instrument lying flat, supported underneath the very top of the fretboard (where it meets up with the headstock), and under the belt hook.
I've tried both, and they both seem to work.
However, I make truss rod adjustments in playing position, because that's when I discover that the adjustments are needed, anyway.

Tuning and truss adjustment should be done in playing position. On the occasion that I've need to do intonation adjustments or adjustments on bridge or nut height, I've done it with the instrument flat on a table.

If you wanted to adjust things in a horizontal position and have them work when you flipped it up vertical - The trick would be I think to lay the instrument across two padded supports in such a way that the instrument length was divided into thirds and the supports met the Stick at the 1/3rd and 2/3rd points. That way you would average out the sag factor of mass in the middle of the ax enough to avoid the adjustments being inconsistent from vertical to horizontal.

Fascinating, thanks much!

Thanks! I found this worked best. I did some experimenting testing the intonation while wearing it and while laying it down in various positions. I found a stack of books just ABOVE the belt hook (so it supports the board) and another stack just below the headstock (so it also supports the board) worked best.

To mention, I found supporting the Stick at the belt hook or lower causes it to bend inaccurately to the way it's worn (I initially had books under the headstock and tail).

At SE there is a station where they have a set up for checkin/adjusting Sticks which is two stacks of phone books and a fluorescent light above it for optimal lighting. When working on the NS they have a "special" phone book to raise the neck side since the body rests on the other end.
Very "High Tech"!...

Sounds good to me!