I know you can't have been bottoming (not even close) before the mod. What you were feeling was the suspention stopping from too much spring.
If the new mounting holes are slightly different side to side you will need to realign the track. Side clearance is tight on th M sleds and AC still uses plain old rivets (stick out too far)to mount the tunnel extention. I run my track very lose and haven`t had any issues.
Remember the sit-in neasurement (3.5in. at the running boards over the rear suspention mount). Might seem like a lot, but is critical to get to the proper shock linkage ratio. Sit down gently lol, and take your measurement. Don`t bounce up and down.
Don`t worry about how it looks or feels sitting still (cause the air shock is a little sticky), but how it works while riding.
Don`t be afraid to try a little lower pressure. 5psi is alot stiffer at the end of travel because the air spring effect is exponential.
I think most people will end up between 80 and 90 psi. 125 is definately too much.
When you have too much air it will feel like it is bottoming (rough) from the first bump on and won`t transfer a well as it can (remember you don`t want it to wheely everywhere) When you have too little air it will feel like it bottoms after the third, forth, or fifth bump `cause of the valving.
It never really bottoms, but that is the best way i can describe it.
I found 2.5 psi noticeable at max speeds but there definately is a 10psi range that is all good.
Once I found my sweet spot for my ability, weight, and speed. I haven`t touched it (pressures) from deep to snowcross (our trails in).