I was advised today that the external linkage V6 boxes are best replaced by another type of gearbox,
Who has done this and what did you do?

Yes, a number of members down south here in Melbourne have replaced the original side linkage gearbox with the updated Type 5 V6 gearbox. These have the gear lever located at the top of the extension and thus eliminate the side linkage arrangement of the old box. This box also has a better 2nd gear ratio as well. It was used in the UK from the update Mk1 models which occurred around September 1971 in the UK, but was never used in Australia models!
 

Thanks for that photo, very helpful. The next question is the obvious one...how do you get one?!

John at CAPRI SPARES (0419 673327) in Brisbane has rebuilt Type 5 with bellhousing and shifter for $1,800.  Uses the same clutch, throwout bearing and tailshaft, no body mods.

Or there is the the Celica/Supra 5 speed conversion.  Dellow make a cast alloy bellhousing for celica, T5, and a few others.  Its a bit more involved as you need to modify a few things like spiggot, crosmember etc