Question 1) Pumping over when shutting off - Sounds like the pump is sucking air into the system during use, could be lack of system head, F&E tank should be at least 750mm above the pump and preferably more,
when the pump the entrained energy is pushing water back into the F&E tank, try turning the pump speed down one setting, although the boiler might protest at this (Kettling)
Question2) Timeclock built in to apollo is obsolete, but you can always fit a stand alone programmer and wire it in to the system & over-ride the faulty built in unit
any decent heating maintenance engineer would be able to do this for you.
Most common parts such as thermostats and Thermocoulpes etc can still be sourced
www.elanar.co.uk, April 2009