Next, the fuse that is specified by Automation direct is a 600A fuse. Do I need to size the wires feeding the drive for 200A or 600A??
Something is wrong here. Are you sure that you are talking about the SAME rating - the motor branch-circuit short-circuit and ground fault protective device as described in NEC Article 430.52?
A 100 horsepower, 460 volt motor would have about a 124 Full Load Amps (FLA) nameplate rating. Even with an NEC allowed factor of 175% of FLA for dual-element time-delay fuses for an AC polyphase motor, that only gets you up to a 217 Amp fuse rating (225 next standard fuse size), or 250% of FLA for an inverse time circuit breaker, still only 310 Amps (from NEC Table 430.52). The NEC table is based on starting a motor directly across the line (no electronic drive in the picture). With the VFD, the starting current is not a problem, so the fuses can be much smaller, probably only 125% of FLA or 200 Amps. Remember, you want to use as small a fuse as possible for safety, but without creating nuisance trips. With the VFDs, your fuses can be smaller than normal, because the VFD provides a soft start for the motor, requiring less start-up current. I would probably use about a 225 Amp fuse because this is a 100 HP pump with higher start-up current. That allows you to use 4/0 cables (ampacity of 230 Amps).
On the load side of each VFD, I will size it for 125% of the motor FLA, correct?
Well you can set your VFD internal overload trip for 125% of 124 FLA, or 155 Amps and get by with a 2/0 wire size (rated 175 Amps). What if your pump needs more current to get started? You might have to raise the VFD trip setting to get the pump started, then you could be bumping against the wire size current rating. I think I would go up at least one size to a 3/0 (rated for 200 Amps). For a 100 HP motor, you don't want to take a lot of chances on having a set of hot conductors.
Remember that the NEC and other standards only specify the minimum required equipment. Good engineering often means using larger than the minimum to avoid problems down the road. This is specially true in plants (assembly lines) where equipment is changed out often. Having larger conductors in places may mean not having a huge added cost of tearing out the old and pulling in new cables.
After I figure out the fusing and conductor sizing for each individual drive, how to I figure out the conductor and fusing rating for MCCB and conductors feeding the power distribution block?
Basically, you want everything to be big enough to do the job, but not so big to be unnecessarily expensive. The NEC requires the equipment that handles the entire load to be rated for the largest expected continuous current. See NEC Article 430.53 for a multi-motor system. The main fuses need to have a rating for the sum of the largest branch-circuit device (200 or 225 Amps for the 100 HP pump in your case), plus an amount equal to the sum of the FLA ratings of all other motors AND any other loads connected to the circuit (without any other factors).
Largest motor:
100 HP Pump fuses = 225 Amps
75 Hp Pump FLA = 96
30 HP Pump FLA = 40
40 HP Fan #1 FLA = 52
40 HP Fan #2 FLA = 52
Other Loads(VFDs) = ??
Control Xformer = ??
TOTAL MAIN RAING = 465 + ??
The 125% factor is applied only to the largest motor in a multi-motor group running off one common circuit, assuming that will be the largest starting current. The other Full Load Currents are only added straight together to the total.
The VFD loads (power used by the VFD itself) would be the differences between input power and output power.