Hi Tex, glad to be of help, unfortunately the mk1 Milltek is infamous for having an annoying drone, its round the 2600rpm mark but disappears just before 3000rpm, cruising at 60mph in 6th gear can grate...
I did look at changing back to standard but just never got around to it, off the top of my head I think the standard back box is around £550, they sometimes appear on here or ebay for around the £150 mark.
The flipside is that it sounds bloody awesome at full chat
It has a far deeper V8'ish bellow. As for warranty I'm not sure, the car was sold to me with it fitted, Sytner's are aware of its presence and I have a copy of the original invoice from when Coopers fitted it for the first owner (I thought that was a bit naughty of them to pass it on to me..)