Well, this problem was somewhat solved for me this turn, as the Pope died of natural causes and I am unexcommunicated. For my empire, I believe that not being excomm. is the most important, because there is a lot of high zeal. My happiness problems have been resolved in one turn. However, the sneaky Italians had some heirs I failed to notice and they invaded two rebel provinces on the same turn I took out what I thought to be their last remaining heir. So it goes, but I have managed to drastically improve my trade and with happiness back to normal, I am at about break-even each turn even with lots of building going on.