Tommy, I can't say that I've seen shrinkage you describe either - even if it had you couldn't be talking about more than 4 or 5 thousandths. Chances are better that you're seeing marks left from removal rather than the actual old footprint. Even if it did, messing withe the moisture content to fit an old footprint before gluing would be absolutely terrible. Intentionally swell wood like that prior to gluing and warp/twist/crack/pop/creep/bow are all immediately invited. It probably wouldn't leave much stress in the joint with the top though, as the spruce on each side will act as an effective stress release when it splits open along the grain.
For removing old glue, yes. Scraping, sanding, filing, whatever means works for you.