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Transposers don't need a timer when placed inline, in fact they close when receiving a redstone signal. Basically they act like a valve where "rs signal off" = open and "rs signal on" = closed.
I figured out something similar, at the very least its easier to automate :)
Here is my system I threw together in creative:
The complete system (don't mind the stuff in the background, it's a testworld)
4 ind. electrolyzers to produce Hydrogen
the reactor with inputfilters for Trit and...