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You ask a lot of questions, but here are a few thoughts that caught my attention.

A 70 on a Montauk is not a rocket ship, so real high mounting gains nothing since the boat isn't fast enough for a surfacing prop to make any sense. The transom design alone will force the engine up about an inch, the bottom bolts coming into the splashwell will determine your height, and I would use the 7-1/4" vertical spacing as Joe indicates if the existing top bolt holes allow it. I would recommend a transom stiffener bar (about $25) across the top bolts, or if you don't want to do this, use heavy duty (from West Marine) 2" diameter 1/2" fender washers at the top. In either case, be sure to use brass nylock nuts on the bolts, either fine or course thread depending on the bolts furnished. This will prevent galling (seizing), a common problem with course thread 1/2" SS bolts/nuts. Course thread brass nylocks are about $1.50 each, but the fine threads can be about $6.00!

Fill in the bottom previous blind mounting holes with teak plugs, driving in and glueing as needed to the thickness of the plywood core, then covered with a polyester resin filler ( such as Evercoat Formula 27) the thickness of the glass, then gelcoated over. Do not use wood dowel. No strength and they deteriorate fast. Teak is tough, hard and waterproof.

DO NOT USE 5200 on the bolts. It is a powerful adhesive not used for this purpose, and if the engine ever has to come off, will take the gelcoat with it! Use Life Seal clear caulking.
For proper sealing of the bottom bolts (important to keep the transom wood dry), they MUST go in form the outside. Slide the bolt though the engine, then apply the sealant to the bolt shaft before putting the engine up against the transom. The top bolts go in from the inside and should be in place also before moving the engine up to the boat. At the engine side, on all four bolts, use M-12 (metric) washers. These are small outer diameter and fit the engine bracket. Conventional washers are too large.

You should be able to download a copy of the engine manual from the Suzuki website.

I think a water separating fuel filter is a waste of time and needless rigging clutter on a Montauk. Boston Whaler does not rig their factory powered boats with these filters at all - not needed. These filters are only for internal fuel tank boats. On deck tanks do not collect condensation. The engine will have it's own filter on it, or if you want double fuel filtration, a simple in-line fuel hose filter can be installed..