BTT

I personally like to glass bed stocks that use through bolts. Not just to get perfect contact, but because the through bolt can pull against the end grain, and the pressure will often create cracks. By glass bedding (even where there's not contact) it strengthens the wood, and helps it survive and avoid cracks.
I do this with all my Ballards that get shot much. It stops existing cracks, and avoids future cracks.

Lipstick works better for hand bedding the butt stock than does a majic marker, just don't let the Lady of the house catch you.

JLouis

I don't like to put any glass on the end of the tank where it curves.  My observation has been that any stock compression at that point can start a crack.  I put 1 layer of masking tape on the curved part of the tang and trim before I apply the release agent.  I want all of the pressure on the flat part when the rifle is set down hard or is in recoil.  jmho

Its unlikely that you can correct vertical looseness on a buttstock like the ruger 1 using the imprint and scrap method.

You will likely have best results by increasing the section thickness on area of the mortise that slopes downward. This is the area that is meant to absorb the recoil.

Here is the procedure I would follow.

Using past wax and an artists brush wax all of the internal parts located between the tangs. Just coat no buffing. Pack this area completely using stiff modeling clay.

Coat all metal work with release agent. 2 coats

Tape off all the exterior metalwork and exterior wood. Coat the tape with release agent. 
Coat your bolt in release agent and the a layer of wax or heavy grease. 

Apply the acraglas in a pile on the middle of that sloping mortise right back to where it transitions to the tang. put a small amount in a pile on the corresponding underside.

Dont apply glass to the area where the wood meets the cheeks of the reciever or the ends of the tangs.

Install the draw bolt but dont tighten it fully tight. Just draw it snug. This will insure that the fit is as intimate as possible when you reassemble.

Glassing properly is 99.9% prep

I hope you don't mind my question, but I bought a Ruger No.1 stock to replace the  factory stock on my Ruger No.3 rifle.  It is a TIGHT fit. The  stock slid on ok with a couple of smacks with the palm of my hand up to the last 3/8" or so inch and then tightened up perfectly on the action with me tightening the thru bolt.  It was a beautiful fit. 
I went to take the stock off to send my barreled action to Steve Durren for some of his expert gun smithing. I had to really slap the stock in a downward motion to separate it from the action.
Now after reading "beltfed's" problem, I am beginning to wonder if I need to do a light sanding on the stock where it fits the action. I am concerned with such a tight fit I might be compressing the wood and setting myself up for a cracked stock.  Any suggestions?

Guys, 
Thanks again for the tips, and interchange.
Did my bedding .
Went out and shot the rifle today- It's got a cal 40-72W
12 twist Douglas bull barrel. Topped it today with my Lyman 20X STS.
Shot several weights of Swiss 1.5 under my new DT cut
439 gr Elliptical PP bullet. 
Very Windy today- gusting up to 25-30mph anyways from 10-12 O'Clock. So shot only at 100yds
Two of the four groups were right at 1 MOA.
Gun feels solid.
Regards and Blessed Easter
beltfed/arnie