Cheap minicell (but thin)
Look for those foam floor mat squares with the interlocking (puzzle piece) edges, usually sold in a pack of 4 - 2’ x 2’sheets.
I found grey ones (sometimes they come in ugly bright colors), in a nice firm density with a nice surface finish on one side, for $10 in the Sporting Goods section at Target. The stuff is only maybe 3/4" thick, but easy to cut and you can get a lot out of the pack.
You could also use the cheaper insulation board from the home center (usually blue or pink with fine grain, or white with the more familar styrofoam beads) to fill up most of it and the uses one sheet of this mat minicell to finish it off so it looks clean and is more durable.
You can see what a smaller piece of this looks like at my album showing my answer to a similar issue in the forward end of my cockpit with space and footbrace issues. Simple - and looks real clean in the boat. Works even better (and have since added a drain channel along the keel line, and a cutout for the last few inches of my bilge pump which rides above my underdeck bag.
http://community.webshots.com/album/103962010nEWiiF
pump
Being a very lazy person I went to Lowes a got an Atwood battery power sump pump it use three D cell batteries and can pump about 10 gallons a minute its mounted behind the seat and does a great job.