I'm going to fabricate the Haynes pedal box , is there any mods when using a bike engine?

It's a cable operated clutch isn't it? If so you should be fine. Might be worth looking at the alternative design one of the guys on the Haynes forum has done though, it's adjustable and the pedals don't flex.

https://drive.google.com/file/d/0B-iOekLVikV5TWdrUEhtZjZHalk/view

Depends on how big ye feet are. Trim out the pedal box and move as far left as possible.

The Avon footwell is not very big. Mine is a bit tight to drive.

I have opened out the footwell a bit, as I'm using the bike engine, I've got around 335mm total width now, I'm going to fab the pedal box as wide as I can and space the pedals out as much as I can

You will need pedal stops for the clutch and throttle, as the bike ones don't need the full pedal travel.