You will need to remove all the existing sealant with a solvent, then use DOW 295 adhesive. Although it is technically a "silicone" sealant, it does not play well with normal silicone caulks, thus it leaks when other things are placed on it, similarly for the window, it needs to be cleaned very well, solvent and or primer depending on the material.
I used sandbags and dive weights and small spacers on the lower edge to keep things alligned properly. On some there is a screw hole on each edge that can be used to affix the glass until the 295 settles, then remove the screw and fill that hole with 295.
There should be a couple of DIY posts here to provide more detail should you need it. ie
http://forums.hunter.sailboatowners.com/showthread.php?p=791596&highlight=dow 295
http://forums.hunter.sailboatowners.com/showthread.php?p=791596&highlight=dow 295
DOW 295 can be bought from most commercial glaziers, and it comes in colors. It is dated and I would not do all the prep and expect good results with out of date product.
YMMV, the prep is the key....both the glass edge as well as the boat frame area
