If you replace the overhead lights, do yourself a favor and leave the existing wires running from the fuse panel to the individual light. It is REALLY HARD to run new wires in the headliner...don't ask...
With everything else, the recommended minimum wire size is 16ga. You can use 18ga for LED lights but ONLY if it is inside a sheath, either protective tubing or as part of a one-piece duplex cable. The AYBC has wiring standards for wire color and gauge here:
http://www.acbsphl.org/Tips_and_hints/ABYC_Wiring.htm
All our old Cherubini boats are wired according to 1970's standards: wires in the bilge, black wires for negative DC ground, non-tinned wire, small gauge, no color coding, fuse panels at foot height.... You might drive yourself crazy trying to match the color standards but as long as you label everything well the rest of the standards are a good idea.
I chatted with a guy on this forum about the new Hunter boats and he said that everything runs through small diameter PVC pipe. I thought that this might be a good upgrade to consider. It'd be easy to affix PVC pipe between the headliner and side of the hull. Put a messenger line inside for future wiring upgrades and it would be a bullet-proof system to be proud of! I don't know about everybody else but I can't stand to see old, sagging wires inside the boat!
PS I put in a new bilge pump the other day and the negative ground had 5 seperate splices in it!