There is no problem with clearing the 5.5" wheel. Do NOT pry between the disc and pads to get the pistons back. If you bend that disc there is only one person to blame. If you can't move the pistons by pushing on the pads only, remove the caliper (again it just clears the wheel) and return the pistons(I use a pair of big snap ring pliers) to their stop. Put the caliper back on the bike before you remove the old pads. This makes for one less thing to juggle or drop.
For another $10.00 you can buy new retaining pins an clip. This is supposedly one reason for brake squeal.
'04 K1200RS Capri Blue(totaled)
2008 Triumph Sprint ST