There is a 1/2 inch of water in the bilge. Normal? Water pump definitely bad. How about a sealed RV pump which may be less prone to corrosion?
There will often be water in the bilge; it leaks thru the hatches. I was able to decrease the amount with improved gaskets. Some have put different hatches in the floor.
Tom From Sea Otter has put in a DIY "dry bilge". I am also in the process of installing the same. It gets rid of the little bit of water accumulation in the pump sump.
My spare pump is an RV pump, but with the same fittings as the factory pump. If you have found a totally sealed RV pump, please let us know the details. Generally the RV are the same as boat. Move it back and up, that will help a lot, also spray with "Corrosion Block" or "Corrosion X" regularly. As Tom noted, we all share the "improvements" we have made in the boats at the gatherings.
The wiring behind the panel is pretty exposed. Is that a problem?
There should be a piece of Naugahyde or similar material which snaps over the back and "hides" the wiring. I rewired part of mine, even though that had already been done. I labeled the wires, fuses etc. Put in a 12 fuse block instead of the 6 which comes from the factory. All exposed positive terminals need a cover over them.
The old Garmin 12 has a big box under the wiring for I guess multiple inputs. Any reason to keep it? It has a antenna on top of roof which I assume is also superfluous now as the Lowrance can read GPS through windshield and roof pretty well.
Yes, I would keep it. We like to put AIS targets on a separate MFD. The Garmin 12" would be idea. The box is an add on for a upgraded fish finder transducer most likely. See how it works before replacing. I always run two or 3 displays. I like to have one large scale over all (for you that probably would be the older Garmin, and a small scale for close up info, the Lowrance 7" (I made the assumption that you have purchased a 7"?). Most Garmin have a built in GPS antenna, but it is possible that yours did not. Check the model number or post it here, and we can tell you. All of the modern MDF chart plotters receive the GPS signal under cover (thru the roof, sides and window). Even two 12" chart plotter could be used on a 25. (I think that John Highsmight has two on his Tom Cat. I have a 9" and 7, and room for another if I wanted. (Use the I pad 12" pro instead; either with Navionics charts, or thru wi fi reading off the Ray Marine MDF I have (Radar, Down Scan, Chirp Sounder, Charts, etc.). For example if we are running in restricted visibility I'll put the Radar on the I pad, and Marie will monitor it. I will keep Eyes on the water, and watch chart plotter/depth.