I have found the problem, nothing to do with drive gain settings or Mach 3 settings.

It was the fuse holders, the Z axis was getting worse, this morning is shutdown completely leading me to check power etc.
The fuse for the Z had been arcing in its holder, the contact between the fuse and the holder kept getting worse until it disconnected the power completely.
So my problem with the replacement Y drive was the fuses and it seems that the intermittent problem I had with the Z going Overcurrent was the fuse holder as well.

I have now pulled all these holders out and replaced them with breakers that have a suitable DC voltage and current rating.

I ran the machine through about 2 hours of rapid moves this afternoon and I have now been running a peck drilling cycle for the last hour with no issues what so ever.

The settings I am running in Mach3 are:

Z: 10000 Vel, 4000 Accel
Y: 15000 Vel, 4000 Accel
X: 8000 Vel, 3000 Accel

I have derated the speed of the z as 600IPM is a bit mad on a 5" axis and I derated the X because at higher RPM's I was getting screw whip and the axis is quite heavy.
The z will run fine at 15M/min and I'm sure that if it wasn't for the screws the X would too.
As you said Mactec I did start with low setting and then work up from there to get to these values (about 6 weeks ago before I ran into the software issue).

I presume that the acceleration value's are fine because my machine is fairly light weight and has good quality linear rails.