please provide a schematic of what you built, with control and switching waveforms
and other pertinent information
use as high a frequency as reasonable possible - 50 kHz is good, higher is better - this reduces the size of the magnetics
(its also outside the range of human hearing and is audibly quieter)
50V to 1000V is a large output adjustment range - you might want to use a tapped push pull primary
two transistors at n turn taps and two transistors at N turns. watch voltage capabilities - crossover is tricky
alternatively, you can build multiple secondaries, say, three secondaries, each adjustable between 50 V to 150V
one has regular diodes and is always on, the other two get controlled rectification, or a an on/off
switch in the form of a controlled FET.
connect them in series and turn on what you need to get the desired output range. crossover is tricky
worst case operation is usually at low input line and high output load, or high input line and low output load.
and you want to safely survive an output short and an output open