Lifting the boat was the easy part, really. For changing out the bunk boards, I just used three jacks evenly spaced on one side of the trailer frame at a time. Put wood blocks up against the hull and gradually raised each one until there were a few inches of clearance over the whole bunk board.
I bolted one end of a bunk board down, used a cinch strap to hold the middle down, and lifted the other end onto the bunk by hand. Treated lumber, which is what you want to use, will bend quite easily. With the free end in position, lower the boat onto the board and it will bend to fit the hull. Then you can bolt the free end down.
Changed out one side, then repeated on the other. Easy peasy. The same method would work front to back. Make sure everything stays stable. Block your trailer wheels well first. Keep the trailer winch taut but not cinched. Do it on level ground, etc. If you want to lift the whole boat at the same time, use cinder blocks and some burly wood for lateral support under the stern and lengthwise support near the bow and near the keel pivot where the boat is strongest. There are numerous threads with pics about it. Floating the boat for smallish jobs is another option. I also have a small lake nearby where I can quickly launch, make changes, and haul out in a couple hours. It's nice to not have to crawl around under the boat.
Regarding the bolts, you can either countersink them through the top of the board so they don't hit the hull and use nuts underneath or use short lag bolts from underneath like I did. Unless you use SS bolts, they will rust, eventually. Countersinks will trap water around the bolt head to destroy it and the nuts and threads underneath will destroy themselves. Lag bolts from underneath will stay drier and be easier to remove in the future if you need to. All they need to do is hold the bunk board on the bunk, they don't carry any weight.
About the surge brakes, not sure what you mean by "...pen oil in the lines to break the paint seal."
My experience with the wiring has been that most problems are at the connections. That and general corrosion of the conductors starting at any opening in the insulation and extending from there along the conductor, especially in the bilge. I'm not positive about the 2nd generation boats, but the wiring in the 1st gen boats is almost entirely laid up in the glass except around the panel and at the junctions where they used three-way connectors but those are painted over. There are schematic diagrams aplenty online, so find the one for yours and identify what and where all your wires are. Then start tracing continuity at each connection from the source outward. Repair any bad connections with waterproof, marine grade supplies so you don't have to do it again.
I'm currently finishing up rewiring my entire boat. Between the new wiring for devices I've added, replacing all the cobbled up feeders, and fixing bad connections, it just made sense to start over and do the whole thing right with modern, marine grade components to ABYC standards. I'll be posting several articles about that project starting in the next couple weeks.