900mL of water is plenty for 50g of powdered bark. The extra lye will help with emulsion, and you could add a little more if you need to later. Also salt, instead of putting all 900mL of water in there at once, take like 100 to 150mL of that water and warm it up, dissolve about 30g of salt in it, then add to the mix. It will help bring DMT over to the aqueous layer and help with emulsion.
I personally shake until the emulsion forms, then let settle. You can swirl to help settle, or set in a warm water bath. I find with all four of the above methods together, emulsion either doesn't form, or separates quite quickly.
and yes you can use cork. I personally use rubber stoppers, have not yet noticed any flaking or contamination, although the shape of one has changed to fit the flask it was stuck in, I think due to naphtha fumes.