Okay so In repetier you have to save every screen or you will lose your settings, and you have to check that it actually saved them. Early on it was notorious for not actually saving your settings. Just go page by page, close repetier then open and double check all the settings. A pain but you only need to do it one time. Then make sure your custom settings are selected on the slice screen.
As for the z “wobble” I know it matches the thread height but it is actually from a bent allthread. Some times you can just flip it over and it will be better, sometimes you can fix the bend. Also tighten up the z axis bolts to try and keep it a little more steady. If it is bent too bad you will crack you z motor mount. Chased this exact problem at a previous company for months, turned out those 8mm couplers do not work on 5/16 rods. Leaves them uncentered and causes the same issue. That is why I chose to print couplers.