Nah - easy to check. Measure current ride height - axle to some convenient point on the tail. Support the bike at the swingarm pivot (and elsewhere to keep it from turfing), allowing rear to be free - lift tail until new height is 1.25" higher. Check for interference.
You could just do this with a couple of buddies - one on the bike to keep it upright, one lifting the tail, one taking measurements.
Probably preaching to the choir, but if you plan to raise the rear 1.25" and have already lowered the front (move fork tubes upward relative to the trees), I'd be a bit careful first time out as steering will be very sensitive compared to stock set-up.
Turns out the 1.25" wasn't possible with the JRi shock anyway. I thought I read that the JRi with the lower eyelet bottomed out was longer than the stock shock and it isn't. After removing it and comparing it to the stock shock it would take 3 full turns on the lower eyelet to approximate the length of the stock shock. I spoke with Greg Spears who was very helpful. He has raised the rear to show 12 mm of eyelet thread which equates to approx. an additional 6.5 mm of shock length or 17.5 mm ride height over stock and has not had a problem with the guide wearing out but of course his racers don't put many miles on

After some testing I ended up increasing the shock length by 5.5 mm which equals 15 mm at the wheel. Less than what I had in mind but at 35 mm sag the chain just clears the guide so it should generate minimal extra wear if any.
I may have not explained the fork tube situation clearly. I have a MT-03 upper clamp and handlebar installed. This leaves 25 mm of tube sticking out the top where the original clip-ons attached. My intention was to drop the tubes down equal to the additional rear ride height in order to preserve the original geometry. Greg suggested that this bike can use some additional rear height in order to improve turn-in. Based on that I left the fork tubes in the stock position and will give it a try next week when I hit the twisties. Whether the 15 mm of extra rear height takes care of the peg feelers touching down remains to be seen. I think there is some amount of feeler that can be eliminated before the pedals touch so there is always that option.
In case it helps here are some measurements:
OE shock eyelet to eyelet center length = 277 mm
OE shock travel = 46 mm
OE rear wheel travel = 125 mm
Ratio = 2.7/1
JRi shock's adjustable eyelet needs 3 full turns out in order to match stock.
The suggested max eyelet turn out needs to leave 12 mm of thread showing.
Marc