4000 watts on a 5500 watt generator doesn't leave much room for anything else. A coffee pot or toaster or microwave are typically at least 1000 watts plus your refrig, freezer and other items. Also an electric water heater has a long recovery time. At the least I'd be looking at a generator that could handle the water heater, well pump, and refrig or freezer (running load not starting load) simultaneously to avoid load coordination issues. Sorry about the advice but electric heating elements (of any kind) take a lot of power... How do you heat your home and cook? Is this a power consideration? As far as the well pump, if the power consumption is not readily available, an external "clamp-on" style meter can easily give you power usage.
BTW - To me any generator purchase is worthwhile. Every time we need to use ours, we appreciate the semblence of normal life and consider it one of our best investments. On the last outage, we had neighbors and friends stopping by just to take hot showers...