The problem with simply filing worn-down notches deeper is that although the "valleys" may end up deeper, the high, flat part of the quadrant is still too low from wear. Team that with an undoubtedly worn flat side on the bottom of the throttle lever and you can see that making the notches deeper will only result in a minor improvement in "click, click, click" as the throttle lever is moved through its arc. And filing deeper notches will not help keep the lever in place until the bottom of lever is built back up with weld and filed.
A more positive stop-gap procedure will keep the lever in place until a proper restoration can be performed. Move the lever all the way to the top of its travel and then take a hammer to the backside of the quadrant "ear". You are forcing that portion where the lever traverses toward the steering wheel. That puts pressure against the lever. Once you have knocked the "ear" upwards, pull the lever down and do the same up top where the lever had been sitting. This will give you consistent pressure against the lever. This works well for the spark lever, too, should it have a tendency to creep while driving. Not as common as a self-moving throttle lever, but it does happen. A slightly improved clicking will be a side benefit. You can then tap the "ear" back to its normal position when you do a proper restoration of the quadrant and lever undersides.
As to your lack of top end, by all means check the timing. If it's too retarded, the engine will not be able to reach peak top speed. Once the timing has been checked, follow other suggestions concerning the accelerator linkage. I have posted this procedure many times before, so I'll only give you a Reader's Digest version here. Have a friend sit in the compartment and with the ignition key OFF, have him/her/it hold the accelerator all the way to the floor. While the throttle is "floored", look at where the carb's butterfly arm stops. It should stop at the built-in peg on the top carb half. Oftentimes because Tillotsons, Zeniths, Marvels and whatever else was handy have been installed, the carb throttle arms are located differently from carb to carb. That means, what might constitute a full throttle position on one carb might only be 3/4 throttle on a different carb. Should your carb have less than full throttle (stopped at the peg), remove the linkage rod and bend the accelerator arm near the exhaust manifold forward a little bit. Re-attach the throttle rod and test again. Keep bending the accelerator arm until you reach full throttle. You may have to re-adjust the idle speed screw once you're done.
Another thing to consider is your speedometer. They are usually off by a few miles in the 45-50+mph range. Still, you should be able to go faster than the 47mph your speedo now reads. That might only be a contributing factor to disappointing top end. Pay more attention to the ignition timing, points gap and throttle linkage adjustment. If your engine is even so-so healthy, it should be able to go past 50mph without self-destructing. Heck, I've driven Model T's that easily went 50mph - and they only have HALF the horsepower as a Model A!
Marshall
Must be a **** beach in the area. 
