That sounds like quite an ambitious project. Do you have any pictures of the area you are talking about. I haven't a clue about the foam tray area under trunk floor you are talking about.
Wouldn't it be easier to move your amp into a better ventilated area? I am sure with the amount of time and the expense in liquid cooling your amp you get a pretty nice install somewhere else in the trunk where there will be plently of air circulation.
Keep us updated on your progress. I would be interested in hearing how it goes.