PEX would be fine- most is rated up to 180F (and can actually tolerate extended use at 200F, but nobody rates it there.)
Even though your new burner is lower output than the previous version it should still work OK with the air handler. Start by setting up the tank for 140F and measure the temp of the return water. As long as it's above 125F it probably won't be condensing (much), but you may need to bump the tank temp even further to achieve that.
If the coil in the air handler proves to be so big that even at 150F storage temp the return water temps are too low, plumb in a "boiler bypass" loop with a ball valve on it to mix in some water from the hot supply into the return water from the air handler before it goes back into the HW tank. You can then adjust the temp of the water entering the tank by the amount of bypass flow. Whether the pump is driving toward the air handler or whether it's driving toward the water heater, as long as it isn't between the bypass loop and the air handler coil you'll still be able to get the full output of the burner into the coil. (If the pump is internal to the air handler unit, as is likely, there may be some dissection involved.)