Chris, I guess I do not understand why you are blowing 40 amp fuses. I run a pair of MFA 850 motors in my 1/48th Fletcher class and use a 25 amp fuse for protection for each motor. I have never blown it, YET, even with weed wrapped props. Neither the MFA 385, nor the 540's should come anywhere near close to blowing 40 amp fuses, even with two motors drawing thru the fuse. Given the size of you build, you should have plenty of power with four 540's which should not be drawing more than 2-3 amps, depending upon whether you are running 6 or 12 volt. 6 amps is a far cry from 40 so I would suspect that something is creating some serious drag on the shafts.
Please forgive me for being nosy, but if you disconnect your motors, can you EASILY spin each shaft with just two fingers? Spin the shaft, not the prop. If it takes any effort at all, there is any issue, as you are no doubt well aware.Good luck with you quest.
Jonathan