Hello there bpounds, and welcome to iBoats. :welcome:
You definitely came to the right place for advice on this rebuild. To answer your question about motor removal, yes, unfortunately you should remove the O/B engine. You will most likely find that the transom is also wet/ soft/ or completely rotted. You'll want to test drill a few holes into the wood low on the transom from the inside to test the wood. As most will tell you in this forum, if the deck is rotted, so are the stringers and transom.
Be careful when buying resins. You need to ask the seller of this stuff if it's suitable for marine layups. I really don't like hoe they call it general purpose. Secondly does is contain wax? Thirdly, how old is it? Most polyester resins have a shelf life of around 3 months. Based on the fact there is very little description of what this is, and the cost, I would steer clear. Most everyone here buys their resin from US Composites. I bought mine from Fiber glass site because they were within two hours drive from my house. The hazardous shipping charges from UPS on resins are a killer.
Save yourself some money by using exterior grade plywood instead of marine grade. ACX, or BCX plywood at Homedepot or Lowes will save you a small fortune. You will be coating all surfaces of the plywood with fiberglass, called encapsulation. Properly cared for encapsulated BCX plywood will last decades. Forget about using 2x4 lumber. Use plywood for stringers and cross members. Plywood is much stronger than dimensional lumber. I'm not sure what redguard is, use fiberglass and polyester resin for all waterproofing. Do not use any treated lumber in your boat.
Good luck in this endeavor. I'll be tagging along to offer any advice I can, as I'm sure others will.