Private van used in Ltd company

I am "helping" out a friend with the tax returns for a limited company. He purchased a large delivery van privately and used this in his own private ltd company. There was no private use of the van. The company ran a straightforward delivery service. He collected and delivered large items. Although he VAT registered he didn't put the van through the company and claim VAT. Can he claim ALL the fuel used in the van and the cost of ALL the repairs & the VAT on the receipts? Also, he was the director and shareholder of the company so can he claim subsistence allowance at the rates allowed for lorry drivers, or does he have to provide receipts? When I asked for his subsistence receipts he told me he threw them all away! I won't tell you what I said to him. Any help would be much appreciated.