Good decision. I don’t really think you can convert 1990’s 2.8 frames to gravel. Their geometry is not progressive at all which makes them well suited as nimble road bikes but rather unstable as gravel bikes. Not to mention that 30C tires (tops) are not exactly gravel appropriate. Even the pros mostly race gravel road sections on 32’s nowadays (Strade Bianche, Paris-Roubaix).
If you start comparing the geometry of the R600/700 with your new gravel bike, you’ll find the latter has a substantially longer wheel base, longer chainstays, slacker headtube angle, much wider tire clearance, and so on. It probably also has no toe overlap which was common with the 1990’s Cannondales.
To lower and straighten your stem it should be fairly straight forward. Unlike modern stems which clamp “around” the steerer, vintage quill stems expanded inside the steerer. Your stem should have a long (usually M5/M6) screw on the top which pulls on an angled wedge inside the steerer on the stem portion that’s below the top headset. Unscrewing this alone will loosen the stem and handlebar allowing your fork to rotate freely (other than the brake housing and cable attached to the caliper on it). Once loose, you can insert the stem deeper into the steerer lowering the height of the bars.
However, before you do this, you should first get your stem parallel to your top tube. Aesthetically, this is how these vintage “symmetric” bikes look best. This usually amounts to a stem with a 17 degree angle (73+17=90). To do so, you’ll find a screw and captive nut on either side of the rotating center junction between the stem portion that inserts into the steerer and the portion that holds the bars. There is even a graduated indicator to show the “angles” you can set the stem at. Regardless, get it level with the TT by bending it down and forward prior to establishing the insertion of the stem into the steerer.
This last adjustment is what will set your stack height and seat to bar drop. The benefit of quill stems is that adjusting the stack is very easy and flexible as one isn’t limited by the steerer length available or using spacers to increase stack as one does with threadless headsets and modern stems.
I should add that you’ll also have to adjust the handlebar angle (and possibly the brifters) once you rotate and lower your stem. For the bars and vintage of the bike, the drops should also be parallel to the TT/ground. Brifter brake lever bottom level with the bottom of the drops.
Before doing all of this you might want to get some penetrating lubricant (e.g., Jigaloo) into the areas that will be loosened as there is a chance that your bolts may have corroded in place if the bike hasn’t been maintained in years (possibly decades). Once, loose, I would also take a moment to clean everything and apply a thin layer of fresh grease on the bolts and wedge junction to prevent corrosion. Your steerer itself should be fine as it’s likely aluminum which doesn’t corrode (it simply oxidizes).
I hope this helps.