Welcome to the Dark Side of the Dark Side, resin ship modeling.
First of all, resin is very forgiving. It is not something which needs to be feared. Many of the techniques which you used on plastic will work here.
See Phil Kirchmeier's article on building a resin subchaser which is in the Articles section here
http://www.finescale.com/fsm/objects/pdf/fpb040422.pdf
1) Fixing the ground-off gouge on the hull: Get some 2-part epoxy body putty such as Bondo or Evercoat. Mix up a quarter-sized blob and spread over the area. It may take several applications to buildup the area. Use some wet-n-dry sand paper (wet sand) to re-sculpt the gouged area. Go thru successively finer grades to feather the Bondo edge into the resin. You may also fill bubbles with a spot glazing putty (Bondo), a model-specific putty (Squadron, Tamiya, Milliput) or even CA mixed with some resin dust. Use what you are familiar with.
2) Prime and paint with your favorite paint type: I regularly use American Tradition Red Primer from Lowes both as my primer coat and as the final color coat on ship hull bottoms. You do not need a special resin paint. If you are more familiar with acrylics you may need to prime, as they do not seem to adhere well on raw resin.
3) Removing parts from wafer pour sheets: These can be sanded off. Use contact cement to glue a sheet of wet-n-dry sandpaper to a piece of glass or plxiglas. Draw around the parts on the wafer with a fine-tip Sharpie or similar (water proof). Wetsand the wafer. Change directions, change hands, change motions. Check regularly, looking at the sanded side and look for the shadow of the Sharpie marker showing through the wafer. When thin emough just snap it off and clean up any burrs with a sanding stick.
4) Removing parts from casting blocks: These are remobed in several methods. Suitablility varies, try and see what works best for you and for the specific situation. A) Back of Xaxto knife: Draw the back of the point of a #11 Xacto knife along the joint. Repeat using increasing pressure. You will plow out a groove of resin. You may have to do both sides. The part will snap off after a few passes. B) Razor saw: You may be able to cut parts with a razor saw or a saw specifiaclly made for resin cutting. The saw does tend to gum up. C) Woodworking saw: I will sometimes use an agressive toothed hand saw to remove big parts. Finish up with a sanding stick. D) Nippers: some pour blocks are almost like plastic sprues and can be removed by using a tool similar to sprue nippers.
5) Many parts can be surfaced glued, without additional locating holes. Check your references for positions. Other parts may require a locating hole be drilled in both the deck and part - and a reinforcing piece of wire or Evergreen installed between them. This becomes particularly important where there is minimal surface area to be glued and the parts may be accidentally struck (ex. boat davits).
6) Consider a building board. This is a temporary base on which the ship is built. Handle the model by the base not by the model. It helps minimize wear to the paint and damage to the PE while finishing the model. I put an upright on one end of the board which allows the board to be laid on its side so I can get to some parts of the model without neding a third hand to hold the model while I work on it.