No need to replace rockers/shafts and pushrods. Check the clearances bretween the rockers and shafts as well as the spacing (end play).
Lifters should be OK with 6K, but you never know. I would try and put it back together.
Measuring the cam gear is pretty inconvenient at home, but it might well be the cause of the noise if the gear that came with the cam was used instead of the factory gear transfered.
There is no O ring on top of the pushrods, there are three on the pushrod tubes, someone got confused. Change them.
The tools for the lifter blocks are only two conical shoulder bolts and cheap, but on the EVO they should be used as the alignment of the blocks determines how the lifters ride on the cam.
Wether you can use stock pushrods depends on many things. If the cam has the same base circle and all the gaskets, ie base and head gaskets, are the same OEM thickness and the head has not been shaved I guess you could, but they are coded and of different lenghts and you really save no labor.
There are two types of adjustable push rods for EVO's the ones called adkustables, and the ones called timesavers. Only the timesavers can typically be fit without removing the rocker boxes, this would change how you put the bloody thing back together. See if they fit between the lifter blocks and head when fully shortened.
Even the adjustables are often of two different lenghts, the long ones go on the exhausts.
To adjust throw the thing together with the rods fully shortened. Lift the rear wheel and with the bike in 5th gear turn the wheel in the direction of travel until both lifters for one cylinder go up and down in rapid siccession and continue to turn the wheel until the piston is at TDC on the comperession stroke, check with a screwdriver thru the plughole.
Now extend both push rods for that cylinder until there is no play and you can just turn them with your fingers. Now turn the adjuster so as to extend them exactly .100" the number of turns or flats depends on the brand of pushrods as they all have different pitch.
Now wait until the lifters bleed down, might take as much as half hour on the exhausts in particular. You have to be able again to turn the pushrods with your fingers.
Now do the same for the other cylinder.
Piece of cake.

It really is a lot easier then it sounds.