All your troubles will be over if you ebay Xuron Rail Nippers [about $7].. They are great.
When you use it make sure the flat side of the jaws is facing the rail you're keeping; concave side faces the unwanted rail..Also, we cut the rail top to bottom (railhead to foot), not side to side. Nothing to plug in/recharge/change blades/tighten the chuck..And it clips the rail off very easily... Do it !!
One tip if you don't already know: If you are going to use 2 or more 3' pieces of flex to form a curve, lay them out straight (on the floor,say), add rail joiners, plug em together and solder the joint/s letting solder ooze into the joiner/s..Why ? Because when you go to bend them on the layout you wind up with a smooth curve. If you don't the flex will form a kink where they're joined and look crappy.. Also: Line up the 2-3 flexes so that the connective plastic between the ties is on the inside of the curve. This allows the outside of the curve to spread the ties out a tad more apart than the inside of the curve as the 1:1 scale does in tighter curves.. Good luck,
PS. Toots (WVgca), Above, is right. Get a little file and smooth the clipped rail ends just a bit before joining clipped rail ends.