The Kernel wont limit the RPM if you use electronic gearing in the drive and with it being a spindle electronic gearing wont really affect things as it would an axis as you will be unlikely to be rotating at very low speeds where cogging would be evident.
You may however not get quite the max RPM out of the motor with it being on an 020 drive so shoot for 3500 rpm and hope for the full 4000
4000rpm x 8000 pulses per rev = 32,000,000 pulses per min divided by 60 = 5,333,333 pulses per second
5,333,333 / 45,000 = 11.85 so a gearing of 1:12 in the drive would allow you full speed if you can get it.
Hood