A starboard or a similar product comes to mind for the companionway sliders and the frame work for the forward hatch then cover with lexan our Plexiglas (can't remember which is the more UV resistant?) The side ports I might just give them a good cleaning/polish and live with them. Another suggestion is to fabricate or purchase deck chocks to secure the anchor or to free up deck space look at the rail mount types.
http://www.westmarine.com/webapp/wcs...&storeId=10001
Bill,