I just installed a new heat exchanger this past weekend. You do need to removed the whole manifold, to get to the two inside nuts. I did find one trick this time, that's worth passing on. This time I didn't remove the exhaust hose, exhaust elbow or saltwater injection on the exhaust. Keep all that attached to the manifold and just loosen the screws securing the aqua-lift muffler so it can swing the manifold to the side. Make certain you have the needed manifold gaskets, you can make the gaskets for the manifold to heat exchanger.
I replaced the heat exchanger with a new one and super happy with the quality. Mine was 34 years old and 20-25 years is the most you should expect. The new one has clean out on both ends, that will make it possible to clean while installed. The old one was in bad shape, almost closed off at one end. The new one is a 3-pass exchanger, making it more effective. Take measurements and make certain you get the right one, Mr Cool was great to deal with. At $299, I thought it was a deal, brand new and made in the USA. A big plus you don't have that stupid rubber cap on one end, mine always leaked.
http://www.mrcool.us/15799-westerbeke-heat-exchanger-17247.html