Is it possable to cut the imput shaft down without grinding the splines off.

Just make a spacer that goes between the bell-housing and the box ala caterham style

The spigot nose on the shaft is a bit longer on the V6 box compared with the standard box but wether you can cut 30mm of and not have the spli es lock the pressure plate is something to look at.
You may also have look at the tube that the thrust bearing runs on, this may also need cutting down.
Would be good to know if this works as it would make the V6 box a straight swap for a standard box without moving the box back or engine forward,
I have fitted the V6 box using the Caterham spacer, if it is done early on in the build there is little difference to fitting a standard box, as an upgrade it effects the prop, gearbox mounts, engine mounts, exhaust exit point and in some cases causes the ancillaries to connect with the chassis.

I thought you could swap input shaft and bell housing's over from a standard box.

no, cos there is a gear cut on the end of the input shaft, and the number of teeth is different