Good to see that you are pursuing getting the best quality out of your images and it will be interesting to see how much improvement via DSLR
Somehow I am not convinced that fluid mounting will offer large benefits when shooting via your DSLR (scanner different of course) - have never tried it other than copying a textured print under glass and liquid to reduce the texture pattern. This is just my theory rather than practical testing...
Shooting with a light source such as your transparancy viewer or even a flash bounced off a strategically placed card behind the film should give you a fairly diffused light source and should be similar to using an enlarger with a cold cathode (diffused light) vs a condenser enlarger. The diffused light source should serve to minimise grain and any scratches rather than enhance as a more point like source would.
As to actually shooting the films then perhaps a homemade copier attachment would offer benefit as it could be tailored to your various film formats. My preference when I last did this (analogue times!) was to fabricate a box similar to the attachment. This is not my original image and I have no idea where it came from otherwise would have given the author credit.
Internal walls black to minimise any flare, aperture cut to match film size and light source flash bounced off a card some distance away from the film set at approx 45 degree angle. Could be as simple and crude as the illustration or more complex e.g. camera mounted on a focussing rail with side as well as forward movement to allow for stepping across the film or just a moveable film mounting solution.