WOW! I was getting the same measurements to the bottom of the bridge. Your bridge must be nearly or completely snug to the guitar. That or your 'top' and my 'bottom' are the same thing.
i have to say, i've been called an ass before, but that's the most creative/guitar related ever!!!!!!!
bro, im REALLY sorry...i saw that i posted 16-18/64 up above, and thought about it more today, so i just referenced 2 of my setup files on my home computer for 2 of my LP's, and they actually reflect 40/64ths on both. you shoud be good to go where you said yours is at.
work injury/pain meds/bad memory/loopyposts.com/hahhaha
it's pretty rewarding setting your own axes up...the more you do, the better you'll get.
i had mine down to about 4 hours total....
-pre-measure 12th(low and high) bridge (L & H), pickups (ditto).
-destring then clean the frets with 0000 steel wool (a good thing to do during fret shine/clean is tape your pickups off with masking tape, theres a whole section about it in the erlewine book). that steel wool dust and residue gets on your pickup magnets...it's a pain. masking taping the pickups is the best way i've found to do it BUT. when you mask off your guitar...you can take the tape strips, and build them as long and wide as you need them. then, i take masking tape, and put it sticky side to the sticky side of the template...that way, you keep a lot of tape residue off your guitar....just seal the edges..hard to explian, but easy to do.
-clean the fretboard (if rosewood or ebony) with steel wool, then wipe the wool residue off with a cotton rag (be carefull with steel wool dust, as it can be VERY painful and dangerous if you blow on it and it flies around in the air). i usually do the steel wooling out on the porch, and try to keep the shit off my skin and clothes, it's kinda nasty like fiberglass insulation.
-lem oil the fretboard then, while that's soaking in, clean the guitar body.
-re-lem oil the board. open the elctronics cavity, flush the volume, tone, switches, jack with de-oxit or even just regular lighter fluid
-if you let her sit for a day or two for the neck to settle, this is where i'd put her down, but not leaning the neck where undue pressure is on it....more, as straight up and down as you can get, or hang it on the guitar tree. some people might argue for or against this, i just always have done it to let the neck flex opposite the string pull. some might argue for, some against this, but, i have done it for almost 16 years with NO issues at all with my necks.
-when you go to get her back setup, you can pre setup your bridge and tailpiece to your measurements. keep in mind, if you change string gauges, things may be a bit off.
-also, a tip to remember when intonating is if the note at fretted 12th is sharp the the saddle needs to move away (sharp/away) from the headstock. then, if the note is flat move it at the headstock (flat/at). i fret my 12th fret notes just like i'm playing normal. intonation can be kind of tricky if you dont have a strobe tuner...i have an old ass accurate as shit needle tuner that gets me pretty spot on, as i've checked my results against a friends peterson tuner.
-if you have a stock nut, the best thing i've found to lube the string slots is a sharp #2 pencil before you string them. i haven't filed a nut slot in a while, but, sometimes when you get those pingers, a MINIMUM filing will do. too much, and you'll be renutting
good luck dude, glad to help. ask anytime, i own 7 gibsons with tune-o bridges...and have set them all up since the beginning. 3 ibanezes too. and im sure, as we've seen, there are a ton of ppl here with different ways and tricks to achieve a good setup.
also,all my LP's have the graph tech saddle string savers. i love them. the sustain increased, my tone got deeper, and string breakage went from about...once a week, to....once every 20 gigs.
sorry for the novel!