We've also just finished our 2nd project and the recommendations really ring true!
Firstly make sure you get on with your builder - you'll be working with him for many months and you need to have a good relationship. Our first builder was technically great and very fast but he did many projects a year and we were just one of his 'sites'. Every small change was a sigh and a bill! 2nd project we had a builder who has been less fast (very slow at times) but I've been happy to work with him. Despite it takes much longer I've felt happier about the whole process.
You can't plan for everything so cost increases are likely - I had a spreadsheet which showed the budget figure for an item and then the actual.Carpets are a good example - until we built the extn we couldn't accurately estimate costs and we were out by 50%.
Consider getting the building regs plans laminated as they can then be left on site without being destroyed.Get separate folders for Planning and drawings, Building regs, Quotes, receipts. The paperwork starts to come in fast once you kick the project off.
Definitely buy cheap builders cups, get a dozen and they will be used. Treat the builders well, we set-up a tea station and we provided biscuits, bacon rolls on Fridays and ice creams when hot weather.You will go through buckets loads of tea, milk and sugar - with 5-6 guys on site we get through over 100 teabags a week!!
Plan for being without heating and lighting for some stages and get plug in heaters. We moved out for 2 weeks during the kitchen demolition to a holiday home and it was a pleasure.
Don' t worry about the children - they seem to treat it as a camping experience.
Portaloo is essential - first builder didn't bother (more profit margin) and it was horrible cleaning up every day after the builders.
Declutter before hand - get rid of any rubbish - we actually bought a small trailer so that we could take stuff to the dump ourselves it's been a great buy.
Building fatigue happens towards the end of any project. You maybe more snappy with your partner so just acknowledge it and look at what you have achieved.