A 26" transom would be good for a 25" shaft mounted on the transom and a 31" transom would be good for a 30" shaft ; this is to get the AV plats somewhere between 1 and 2 inches above the bottom of the V. If you have a jack plate with 5" setback you could probably go a couple of inches above that.
Laying glass can really be done from either side - I would probably do it like I described because it seems easier for me to get a good finish - that said, I don't know your exact transom arrangement or skillset with fiberglass and resin. I consider myself to be a learner with a long way to go in that area. The big thing is to make sure the inside skin can handle a lot of tensile loads that come with an outboard hanging on it - especially with a jackplate which gives it a bigger lever.
Also - plywood weights: Okoume and Meranti (I think Lloyds certified too) are both pretty close to 26lbs/ft3 like Coosa Bluewater 26 and unspecified 'marine' plywood is more like 30-35 lbs/ft3.
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