My main one would be for you to to visualise yourself in each of the rooms impacted by the build and ask yourself what do you expect too see when the work is completed then write it down as a bulleted list, Then agree with the builder what's in / out of their quote.
Electrics - Give yourself wriggle room. ie. specify x stainless steel finish double plugs in y room, exact location to be agreed onsite. New fuse board?
Woodwork - Think of matching current in terms of doors, skirting, coving, architrave etc.
Plumbing - what sort of heating control to you want e.g. separate zones. TRVs? Water softner? Upgraded supply?
Outside - consider sockets, taps, paths, retaining walls, lighting, making good of drives
Other - If you supply things for them to fit, be there when they open the boxes (or open them yourself). Our claimed that stuff had come damaged but I think they were bull-shitting me but couldn't prove either way
Payment - pay by outcome / stage, not by time or 'I need to pay the lads something this week'. Keep a reserve pending final building, gas safe, electric, hot water tank certificates. Also any guarantees where they've subbed out the work - rendering, windows, external doors
Agree what happens to stuff they're stripping our - theirs to sell or yours (we had some copper roofing that they thought they could sell)?
Most of all, keep on top of them about progress - I found daily meetings good idea if only as a set time to discuss things - what's next, what decisions do I need to make (and make then quickly!)? Be reasonable, things change or crop up that's unexpected and can sometimes give rise to additional cost. When they give you a price for these, have a sense of what the right day rate is for the skill in your area (e.g. carpenter £150, plumber & mate £300 etc)
It will be stressful, it will take longer than you think, it will (probably) cost more than you think, they will be messier than you think, they will be inconsiderate of you and your neighbours and they wont turn up when you're expecting them (Saturdays especially). But, once they've been and gone and some time has gone by, it'll have been worth it and you'll soon forget the negatives!
HTH! (I had a really crappy build by the way, partly down to the builder, partly as things cropped up that no-one could have foreseen)