When you bypassed the fuel reservoir, you did connect the two smaller hoses and the two larger hoses, right? Just checking, because the supply and return lines switch positions when they exit the reservoir. Swapping the lines would create the problem you have.
Also, if you try to force open a reservoir that was not designed for a filter it could break it. I have heard that the two parts of filter-less reservoirs are glued together.
IMHO, I would leave the reservoir connected. Unless the low pressure pump in the tank is only needed for priming the system in your new configuration, it may not be able to keep up with the volume of the high pressure pump.
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