jc12 pointed out a very good tip, to just cycle with straight RO. Monitor any changes easily as you know the water is always the same, instead of juggling mineral content with remineraliser.
It's true, the BEP was never intended for shrimp, but was popular by shrimpers because of the 'buffering' affect it has. I'm still a big fan of BEP as ive never experienced a bad batch and ive gone through 6! Benibachi has also been good for me too.
It may not be the issue, but how old is your TDS meter/pen and what brand is it? 350 is super high, if you have access to another tds pen to compare to it could rule out a faulty tds pen or which needs calibrating. Just a thought ?
Rinsing the substrate wouldnt be a problem though, or atleast a big one. It's clay based if im correct, and in the aquarium lasts quite long. abit of rinsing cant hurt i reckon.