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As the owner of a couple of 70's Whalers with shallower splashwells, I agree with what Tom and Joe have said. Clarifying a little. here is how I have done it. But anyway you look at it, the engine is going to be mounted higher, but not so high as to not function. You may have to spend a little more for a good SS surfacing prop however. With the mid-range Mercs, 75-125 HP, you are in luck, as for some reason Mercury designed these 20" shaft engines to be longer than 20". So they can take quite a bit of extra height.

After filling in old holes, including those terrible blind hole mounts that OMC used (and Yamaha copied), What I do is measure how far down the bottom holes can go in the splashwell, and still enter the splashwell on a perpendicular
basis. Using a 1/2" standard washer, hold it on the inside of the splashwell where it will lay flush, and trace the hole onto the transom. The centerline of that hole is your controlling dimension for the top hole of the bottom set of holes on the engine. You can then transfer that dimension to the outside of the transom. Normally, per Merc's recomendations, this centerline would be 9-7/8" below the top of transom. Your measurement will likely come out something near 8-1/2", which means your engine will be up 1-3/8", and can't go any lower than that. This is good, and works very well for the longer shaft 90 Merc. Even 1/4" higher will work also, as I mentioned.

Now that you have the bottom holes positioned height-wise, you have to determine where to drill the top holes. EVen though the engine manufacturers recommend 1-7/8" below the transom top, you can go higher, to about 1-1/4" if necessary. Here I would use one of thse transom stiffener bars. Obviously, the BIA vertical spacing of 8" won't work, but the next hole down on the engine, 7-1/4" may, and the next one down, 6-1/2" above the bottom holes, will definitely. So you can decide which to do if you are mounting directly to the transom.

If you want to use a jackplate, I recommend an anodized aluminum Detwiler, since they come factory pre-drilled with two sets of holes, 1" apart vertically. This allows you to use a 7" vertical spacing, which works well on these older splashwells. Here is photo of mine, using the Detwiler 7" vertical spacing:

http://smg.photobucket.com/albums/v42...G_0356.jpg