The clicking can be solved by stopping the actuator arm from moving up and down the shaft ie. with washer(s)
The trick is to place the washers so that the piston goes directly into and in line with the master cylinder -although this is impossible because one part 'swings' and the master cylinder is fixed in position.
if you remove the inside of the eyelet of the actuator arm, it is a little brass barrel. It gets deformed in shape, when there is pressure from your foot moving the pedal. I took this bit out, but just stopping the eyelet moving should be ok.
To help with overall alignment, I loosened the master cylinder, where it secures against the bulk head(?) and used a tiny wedge to point the cylinder in a better direction.
I would also lubricate inside the cylinder. Get an aerosol can with the applicator straws and poke the straw between the rubber and the piston (under the silver covering in your pic). I tried all kinds of lubricants: wd40, lithium grease ....none worked for any length of time but copper grease has kept it lubricated. When these cylinders get old, the feel becomes notchy and the lubricant gets rid of that.
Its a pig of a job to change these apparently, so I would try to preserve it for as long as.