I had a similar problem but not with the pex line My valve on the toilet was leaking and needed to be replaced. What I did so that I could continue checking the rest of the water lines was to disconnect the line at the toilet valve and put a 1/2 inch plug in the connector fitting. I had a few on hand from when I had my pop-up. They do come in handy and may help you get through an emergency. Also like your idea about adding shutoff valves.
2004 Jay Feather 25E
2001 Ford Expedition 4X4 EB 5.4 3.55 rear
2004 Ford Expedition 4X4 EB 5.4 3.73 rear