OK... please recap exactly where you are at... gfi still tripping with all applicance removed? also furnace fuse blowing? These are potentially two issues... maybe. The GFI circuits typically only involve 120v while the furnace only involves 12v.
IF GFI is still tripping with all stuff along its circuit path unplugged, then its likely wiring leaving the gfi going to the various plugs. You need to disconnect (and inspect) the wiring at the next plug in the "daisy chain". Once disconnected at the "next far plug", does the gfi still kick out. If not, then the issue is further down the "daisy". IF so, then the issue is between the GFI and the disconnected "daisy". You repeat the checks by connecting the "daisy" moving to the next "daisy" in the chain. In terms of physical checks, you are looking for some aspects that is likely "bridging" the neutral to ground in the wiring / boxes along the chain.
In terms of the fan, potentially check your thermostat / wiring there of. If possible, disconnect the furnace control border and see what this results in terms of the fuse.
Of course, it is not obvious how these are specifically related to the microwave "incident". :-( Although possibly the ground fault has caused an issue in the furnace control board / motor or viceversa.
