I had to replace the seals in my 04 FJR years ago when the front wheel wouldn't free spin more than 1/2 turn.. After new seals, easily 3.5 full spins..
Rubber seals with age, harden up and don't flex (and retract the piston) as would new seals. I didn't have any leakage...
I have the exact same calipers on my FZ6 as the Gen 1 FJR has. Same issue, with time, free spin was down to 1/2 to 3/4 a turn.
*Another easy way to check is to go for a ride, stop with the REAR BRAKE ONLY, and then touch the front rotors. If their dragging, the rotors will be hot (not good).
For my FZ6 (don't have the shop manual for the FJR anymore), seal replacement, by Yamaha is recommended EVERY TWO YEARS.
In real life, I've found 4-5 years more realistic.
Re popping out pistons. If you have access to even a small air compressor, a pointy blower tip WITH an angled cut of rubber hose on the end takes care of business. Simply put the hose on the tip, have it trimmed to an angle, then slip it in the bore(one piston is popped out hydralically). Add a shot of 100 PSI or so, it will come out. Put a rag in between the piston and the caliper to prevent damage/ flight and
definitly watch your fingers..