iroctd wrote in post #18542971
Canon sensor assemblies have alignment pins. You can see these in the photo of step 12 as black circles next to the screws with the red arrows. And again on step 14 you can see the double holes, one for the pin, other for the screw. These posts do not allow any adjustment so it goes back in exactly how it came out.
They sometimes use shims for front/back focus adjustment. As long as you keep track of where they go (which they are easily held in place by the alignment pins) it isn't a issue.
exactly - main problem I think would be if a shim stuck to the sensor frame during removal rather than staying on the post, then falling off before having it's position noted.
From what I gather, Canon techs use some sort of micrometer to measure the "flange back" distance which is the measurement from the lens mount back to the sensor/IR filter & adjust thickness & number of the shims to get it within spec and the two nice and parallel with each other.
iroctd wrote in post #18542971
Remember their techs that do these repairs are people like you and me with big fingers and screwdrivers. They've made servicing them quick for profit and efficiency. If it was that critical they would spend too much time fiddling with adjustments.
I think the Canon techs replace components as modules rather than actually repairing anything - 3rd party techs would replace an individual leaf on a shutter for example, whereas Canon would swap out the whole unit. Same with hotmirror/IR filter replacement.
Just to put repair things in perspective, when I modified my 10D to IR a while back, the screw heads holding the hotmirror/IR filter bracket just sheared off instead of playing nice and unscrewing, I needed to drill the two screws out and retap the thread to take a new screw while being careful the swarf didn't foul up the sensor itself to get it sorted... 
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End of the day, if the OP's sensor itself has fungus on it, then it's going to be an entire sensor replacement needed (which also involves alignment measurements & shims), but if it's just the hotmirror/IR filter that's affected then it is possible to achieve quite a bit more easily, just not by Canon.
some fairly old canon camera stuff, canon lenses, Manfrotto "thingy", and an M5, also an M6 that has had a 720nm filter bolted onto the sensor:
TF posting: here 