Hi Richard!
Heel-pannier interference can be caused by many things...placement of the dropout eyelets, rearward offset of the rack and its crossbars, but mostly as a result of chainstay length, crank length, and of course...foot length and their placement on the pedals, and even pedaling style (heel up, down, or level). On the panniers themselves, shape can make a big difference, as can the placement and adjustment of the mounting hardware.
I had no problems fitting and clearing my 40liter Ortlieb BackPacker panniers on my Sherpa, but it was a Mk2 560S, a bit larger than yours and with longer chainstays. The MegaBrochure lists a Sherpa Mk3 in size 500L as having 438mm chainstays. My Mk2 560S had chainstays 445mm long, so a 7mm difference. This is what you would also get if you went up a frame size. Would that 7mm make a difference in clearance for you?
There's a number of remedies that can be tried if adjustments allow: Placing the bags rearward and higher can help, as can tilting them if the mounting hardware will do this. On one of my randonneur bikes, I needed a Tubus Logo Evo with its secondary, extended mounting rail to get the panniers back far enough to clear my heels. On the other randonneur bike with 429mm chainstays, the rear panniers mount on lowrider frames attached to the rear rack. If I hold my foot horizontal when pedaling, my heels strike the panniers as well as the lowriders. However, with my high-cadence style, I lift my heel just in time to avoid a heel strike in practice. A lot of my clearance depends on saddle height. If mine were lower, my heels would be also. Fortunately it all came out right for me on that bike, but have you checked if your saddle height is correct for you?
56 liter bags are pretty large, so I would expect to have more clearance issues with them, but the 40 liter panniers should be much easier to fit. Since they also have clearance issues, I think the solution may be to move the bags rearward if you keep this frame size.
Richard, is your foot placement on the pedals any different with this bike? Are your crankarms the same length as your past bike? Are you using different shoes?
Best,
Dan.