There is a product that I've used successfully on the lower and upper bays of my house....
Dry Fix & Dry Flex
http://www.window-care.net/
Head Office on 01487 830311 for details of your nearest distribution outlet. Dulux centres sell it.
Check out the Case Studies...
There are three different product types 1, 4 and 16 which describe the setting time in hours.
For each type 1,4 & 16 there are two preparations a sealer primer in 2 parts - Dry Fix - and a Semi flexible resin filler in 2 parts Dry Flex.
You dig out all the rotten timber (I used a router bit in a drill) and paint it with the sealer primer. After an hour you mix up the resin filler and slap it in the voids and use it to permanently fix the replacement sill.
It's very sticky stuff and vinyl gloves are essential. Set up costs can be steep - you will need the special two tube dispensing gun, Set of plastic spatulas, Sealer Primer and resin filler. You can mix it up on any old sheet of stiff plastic or perspex. Clean up with meths.
Expect to pay about £120 - mine was a big task and it cost me £300 in sticky materials but saved me several thousands because I did not need to replace all the windows with new ones!
You need to arrange for a "bed" of resin of at least 4mm between components. Make the new wooden sills oversize if you wish and shape them to the correct matching profile when the resin dries.
More pictures here...
http://www.woodcap.co.uk/index.html
I can not reccommend this product more highly - I have no financial or particular personal interest in singing its praises.
Peccavi, April 2009
