no problem refitting wheel, axle clears silencer, its just the head thats the problem, well on my 125 at least, last 3 inches or so. when I get close, pop bike off stand, lean on seat and tap back in, I use small wooden hammer, pop back on mainstand and proceed as normal. shocks completly standard.
this is a typical problem on the early ones, yamaha wanted silencers tucked as high as possible.