Last week I took the old windows into the Engineering Workshops at work, to see if they could replicate them. I picked them up today-cut to shape, with all holes drilled for £10. BARGAIN!
They used 6mm clear perspex for this andI've had them made 15mm bigger all round to enable me to bolt them on, using stainless steel screws on a bed of clear silicone.
The old method was to use window "Rubbers" much like in cars or old caravans but apparrently this method leaked a lot. I also think the bolt-on method will look much smarter.