My understanding..
Unfortunately if your builder isn't registered for VAT there isn't a way for you or him to reclaim the VAT paid on materials.
Nor to any subcontractors... So if your builder hires a VAT registered subcontractor, like an electrician, the electricians bill and any materials he supplies will be at 20% (to your builder). However if you were to hire the VAT registered electrician directly he can 5% rate everything to you that he supplies. This is because the 5% rule only applies to labor and materials supplied to the "final customer" by the person/company doing the renovation.
If it had been empty for 10 years, and the builder was VAT registered, you could also claim the 5% back charged by the builder AND the 20% you paid on any materials using the self build reclaim scheme. Unfortunately I'm pretty certain this doesn't apply to properties only empty for 2 years.