Rear shock is easy to do, just a bolt top and bottom unless ESA (which just needs unplugging).
Use heat on the lower swing arm casting to soften the Loctite.
Bolts are not stretch so can be reused. Keep them separate, don't mix the bolts. The lower bolt has a different pitch IIRC and if you put the top bolt in the swing arm hole it will chew up the threads and seize, possibly scrapping the swing arm. I felt mine seizing on tightening, stopped and removed, retapped the casting and got away with it after realising my mistake.
When refitting, there is a steel sleeved bush in the lower swing arm casting that can close up the 'eye' of the shock mount, meaning you can't get the shock back in. I had to use an oversized socket as a cup and nut/bolt to draw the sleeve back into the casting to provide enough clearance when refitting.
Check your swing arm bearings, these commonly corrode and wear as they are not fully sealed. Easy enough to replace with the swing arm out.
Also grab the final drive with the rear wheel airborne and try to twist it sideways at the hinged joint. The trunnion and needle rollers can wear allowing play in the FD to swing arm joint and wheel misalignment.
As an aside, the knocking you heard/felt could possibly be your brake pads rattling about in the calipers. I've had weird noises and knocks from both the front and rear pads on my bike in the past. In Riva Del Garda I had convinced myself that my driveshaft was shot and I couldn't ride it home from Italy. Close inspection found the rear pads were bouncing in the caliper casting as the spring shim above them had broken.