Without giving away my age, this thread reminds me of when electroic ignition was first introduced in about 1975. Prior to that, almost everything, 2 and 4 wheels, had points and condensor. I remember that many owners (mostly of cars/trucks but some motorcycles) had the electronic distributors converted back to points. This way every 3000 miles they had to be adjusted and the engine still had same cold-starting problems experienced for the last 75 years.
Yamaha is doing us all a favor by providing ABS and even linked brakes. 95% of street riders will stop in a shorter distance with this technology. Sure the braking distance numbers published in MCN or other magazines for ABS/Linked brakes are slightly longer than conventional braking systems but that is because the "tester" knows how to stop (on dry, clean pavement) with out locking up the front/rear tires.
I spent many sessions with MCN in the CA desert working the radar gun and watching and learing how to make fast stops. I've been riding for almost 40 years and I still could not equal the stopping distances of even the ABS bikes, let alone those with conventional braking systems. The only riders that can stop faster than ABS/linked brakes have had extensive race track experience. Remember that the race tracks normally don't have oil, leaves, sand, anti-freeze, gravel dear ****, etc... on them. On the street--you can ride over almost anything when you apply the brakes.
If you're going to "de-link" this new FJR braking system why stop there? Get a set of carburetors, a set of dual-points and some old ignition coils and change everything out all at the same time. Throw away those radial tires and get some good bias-ply--they'll last over 15,000 miles with almost no tread wear. These changes will allow your new FJR to perform as well as any motorcycle manufactured in 1975 and you can sell all the replaced parts on eBay.