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Ask the architect about using the RIBA contract. In my opinion it is more in favour of the home owner, the JCT contract is in favour of the builder. RIBA is really mainly in favour of the architect, who is god, but I would expect you and the architect to be more often in agreement than you and the builder. There isn’t a “homeowner” organisation that has a contract that is actually in favour of the client as far as I know.
I would not use the JCT contract.
Yup, that’s pretty standard in traditional JCT Contracts but definitely the way to do it for anything of a certain value/size. Works valued on a monthly basis with 5% held back. 2.5% released on practical completion (ie: when the scaffolding is removed in the above example/works signed off etc.). 2.5% held back for 12months to rectify any damages resulting from movement/settling etc.