Clean and polish the fuse clips. Verify the clips can still pivot to align themselves with the fuse for maximum contact surface area between fuse and clip. Check to see if the spring clips have lost their tension. They should have a really firm grip on the fuse. Check the solder connections on back of the fuse blocks. Poor connections here can conduct heat to the fuse.
As you know, a fuse will melt when it's current rating is exceed. The fuse is always generating some heat whenever current flows through it. More current = more heat generated inside the fuse.
The bike in stock form had plenty of margin between normal run current draw and the point at which the fuse melts. 3 ohm coils draw about 40% more power, through that fuse. And, while it is not enough additional to melt the fuse outright, it will run in a warmer state than with the stock coils. If you add contact resistance heating, poof. In theory, you should increase the fuse rating by two or three amps. That should get the normal run fuse temps back to where the factory designed. Remember, though, that the factory used new, un-oxidized fuse clips, too. Also, if you have added lighting upgrades that draw more power, these increases should be added to the fuse rating, too.