Capt Bill is 100% on, remove the screws in the transom anyways, silicone is not the right type of sealnt for those screws, more importantly if there is no transudcer there anymore they should no longer be there to fill the holes, the holes should have been epoxied over. If the ducer is still in use, use 4200 to seal the screw holes, although personally I like to drill holes(slightly bigger then screws to be used, fill them with epoxy throughly and then drill your holes for the screws and seal the screws with 4200, the epoxy will waterproof the transom so even if water gets in thropugh the holes, your transom is safe, you might just get a drop or 2 in the bilge. If you are using epoxy and 4200 you should not have a problem at all and it will last longer then the transducer will.
Before you remove the screws, make sure you drain the boat first by tilting it up and removing the plug, once you feel all the water is out, then remove the screws to see if your transom has water in it. If it dribbles out you have a transom issue that needs quick attention before it gets worse or your transom fails, especially since you repowered recently. Did your yard who repowered you check your transom, a good yard will ALWAYS do this as a precaution, but a lot do not...they should be doing so though unless they do not care about customers or well just do not put the extra effort in.
As far as weighing the boat, Grady's weight does not include any extra's, batteries, bimini's, hardtops, etc so it would be really really tough to do this and really tell if your boat weighs more then it should, plus you need an accurate weight of the trailer and to know the exact amount of fuel in the boat, things most guys cannot get or know exact enough to do this and get any real concrete conclusion from it. Good idea, but hard to conclude anything from it in reality since there are too many variables and too many unknowns or close guesses.
As far as the boat sitting lower, I repowered a 1989 22 seafarer with a 200 HPDI from an evinrude 225, engine was 96 lbs more I believe, plus all new rigging, bigger oil reservoir, and the boat dropped almost an inch at the transom, at first it seemed low to us, but with full tank the bottom edge of the scupper just barely touched the water, and when your out in any seas drifting or anchored, they would get covered at that depth or sitting an inch higher. We did have to get used to the new feel of the boat, but never felt it was dangerous or close to that, we had plenty of freeboard and had no issues draining the cockpit or with waves flooding it or water ever sitting in it, it was just how it was with the previous engine. Did you have the boat full of fuel a lot, or laoded any differently previous to the trips where you felt it sat lower at the transom? Any new accessories or new/bigger batteries?