I think I read somewhere else that the newer more compact caliper was fitted to a number of brands around the same time to save weight and would explain a bit of the flex issue.
If you have swapped the MC over, check the bore, I had a 1/2" (12.7mm) from China vs 11mm standard, brake felt firm (wooden) but performed poorly with the 1/2" MC.
Piston Dia of the Caliper may also have changed, your XR caliper has 27mm pistions, I think the newer GG caliper is 25mm (was on rear, never checked front).
The reduced dia of both the MC and Caliper pistons equates to a much higher clamping force that could emphasis the flex and add to "soft" lever feel.
My latest setup is standard caliper and MC, brake switch removed, lever feel is ok-good.
Biggest improvement has been a set of S33 offroad pads, I had EBC reds on previously and had to really pull the lever to slowdown, which leads to flexing etc.
Brake is now amazing! plenty of modulation and enough to lock up/endo with 1 finger.
http://www.goldfrenusa.com/brake-pads-S33-offroad.htm
worth a shot