(for example, after a good thunderstorm, the wireless link will be down for at least 12 hours, but will fix itself eventually.
Are you sure there's not a moisture problem in the antennae cabling? Get an SWR meter that can handle the 2.4 GHz range and make sure that SWR is very low (approaching 1:1 but certainly less than 2:1). Hook up the meter in-line at the AP. Test this after everything is wet and again when there's been a dry spell. Minimize the number of exposed connections and use dielectric grease. Any exposed connections should be well wrapped with that rubberized electricians tape first, then with regular.
Resetting either access point will keep the link down for at least 30 minutes.
This seems to point to signal quality issues. This could be interference as others have suggested. Few things to try (in order of less work, less $$$): 1.) Try different 802.11 channels. Pick one of 1, 6, or 12 as they are the only non-overlapping spectrum. Set this manually on both ends 2.) if yaggi type antennas, try changing the polarity. If it's vertical now, try horizontal or vice versa (both ends should be the same for maximum gain!) 3.) Try even higher gain "dish" style antennas (these have circular polarity) 4.) Use APs that do 802.11a or n. These are much less susceptible to interference. This probably also means changing/adding antennas. *.) Bonus idea: Google roll your own dsl (assuming both locations have the same CO). Basically: get a dry pair (no dialtone) from the telco going from location A to Location B; buy two sdsl modems and install at each end; hopefully enjoy a few-several Mb connection! ~JasonG