A foot at 100 yds is considerable, no doubt.
Much depends on how the action/barrel sat in the old stock compared to the new one.
I, too, have a Rem. 700 Varmint in 25.06. One thing to note is that the original Remington stock almost certainly has a pressure point built in at the tip of the forearm, the idea being to control barrel vibrations. (Sometimes this works, and sometimes it's a major source of grief, particularly on wood stocks that are affected by temperature and humidity. When in doubt, float the barrel!)
If the stock you switched to provides for free floating the barrel, this almost certainly accounts for the significant vertical change in point of impact. With the original stock, it should take no more than about 10 lbs of pressure, max, to separate the forearm from touching the barrel. That you get a foot of vertical drop leads me to suggest that there's far too much pressure against the barrel...especially considering that it's a heavy varmint barrel!
That aside, here's something to pay particularly close attention to when reassembling any Remington 700 action back into a stock, something that's all too easy to miss, believe me!
The magazine, made of spring steel and split at one end, can be a tad tricky to seat between the bottom metal and the action properly. If not properly done, it can bind between the two, and thus create fairly substantial pressure against the action. You might even see the bottom metal...being the cheap piece of junk that it is...actually bow at the center from this pressure!
To determine that the magazine is properly installed, you should be able to generate a tad bit of vertical play in the magazine...maybe 1/32" give or take...between the action and bottom metal. IOW, the magazine should, and must, float freely!
I replaced the bottom metal on mine with a Williams made of steel, which is about a kabillion times better quality. The cutout for the magazine is much deeper, and pretty much eliminates this potential problem. The inset on the original is shallow, and thus the magazine tends to not stay in place when reassembling the stock to the action. One has to be particularly careful with this.