Hi LongSFMI,
As stated I have an O&G background so obviously my thought process is always to go from the top down. But either way I agree with both you and spiny that draining the water out of these shafts should not be a huge technical challenge. Without knowing a mine plan which is the best way to go I do not know. As spiny said if you go from the top down the shafts will probably have to be drained and reconditioned in stages. If you go from the bottom up once it is drained any new shafts going up will also have to have infrastructure installed. Either way being through granite with its inherent natural stability will be I think a huge benefit.
As for clogging I do not see this as to much of a problem either way you go. There are various layers of different size screens which can be attached to any inlet plus if it was me who was designing the system I would make sure there was some way of back flushing to keep the screens clean and open. With an ESP at this depth it is easy. You do not put a one way check valve above the pump. Then just turn off the pump and the normal hydrostatic pressure of the water just flows backwards down through the pump and blows the screens clean. Working with the type and size of ESP required to pump from this depth and pressure will not be difficult.
Regards