Adding cursors to analog oscilloscope
Sounds right to me.  Measuring the A-width is something a bit extra, as the necessary timing is sort of independent of the width.  Remember, you're putting up a "cursor" because you have interest in labeling some time point (which you don't need the width for) -- not some location on the screen (which you do need the width for).  

You shouldn't need to program in assembly for accurate timing, but you might consider using timer interrupts.  

For controlling the location of your Z-pip, you can certainly use a pot, but you can also use a frob-knob (i.e., encoder), up/down buttons, a keypad with a display, or anything else you find convenient.

Nice project!!

Not a great call on using the A as a clock, even with a PLL. Use a fast clock, trigger an interrupt with the rising edge of A.  Also use A to gate a timer, so you know your sfreen width.  PWM will be more difficult than just turning a pulse on and off, maybe with a CCP interrupt.