The 20 amp fuse is what supplies the power to the PTO, among other things. If your PTO has its coil potting compound or insulation breaking down internally, the coil might be shorted or partially shorted. Measure the resistance of the coil on the PTO -- it should be in the range of 3.5 to 4.7 ohms, give or take. If it is very much less, it could be the culprit in blowing the fuses...
There are other places in the wiring harness that often get shorted to ground, like the seat safety switch, but it receives its power through the 3 amp fuse. The headlights however are powered from the 20 amp fuse...but if the light switch is off, that wiring should not be a factor, regardless of its condition.
Did the fuse ever blow when the PTO was not engaged?