Quite a lot of the time I'm able to get large parts of seeds by hitting the shell against the ground. This causes bigger cracks in the shell than the seed, I can then pry off the outer layer. However, I've never been able to get a whole seed this way.  The only other ways I can think of would be dissolving it in an acid or using abrasion, but I do not know if these would work.  What is the best method of removing the dark outer shell from a coconut without damaging the inner white seed? 
The amount of sugar in this recipe looks a bit low for a 10 minute simmer. I estimate that the bulk of the ingredients consists of,   ~200g sugar ~330g cranberries ~330g bell pepper   That's less than 25% sugar. If this were a straight cranberry jelly, you'd need about 40% sugar content for optimal jelly strength and, I estimate, at least 35%.  I think that you could add another cup of sugar, bring it back to boiling for a minute and then let it set again. If you don't want to risk changing the recipe you could simmer longer until the pectin is fully precipitated (at about 220ºF or 104ºC according to the answers on this question)  Update: One of the answer comments on the question I linked to suggests that 220ºF is an indication of optimal water content, so it may not relate to pectin precipitation. TFD's answer has a tip for testing "pectin levels" with methylated spirits which might be what you need. 