General tips

We'll do this as a running list which we'll add to as things come to mind.  They should help broadly with most project builds:

• Confirm everything in writing, and get an early understanding on what they'll do for you if they get things wrong.  That's everything you say during each stage.  It includes confirmation of responses to your questions.  It'll be a right pain early on but it's important.  Confirming something in writing won't necessarily get you a good outcome, but it will stop any passing of the buck and at least give you negotiating leverage. 
• A great example is that we had confirmed in writing that our build time was 36 weeks.  Fast forward to final signing of contracts and we're advised the duration is 45 weeks.  The extra 9 weeks was justified our Alkira's part by the fact that we were building an Elyse 15 (larger two story home) and that we'd made a few variations to their standard build.  We confirmed the 36 weeks in writing after selection of the Elyse 15, so a 9 week addition to timing guidance was their mistake.  Whilst we had this in writing, when you're already deep both financially and from a time perspective in to a process, they know they have you over a barrel...  we complained several times but they refused to either change the contracted duration, or compensate us financially.  Bear in mind that the 9 week period is 9 weeks for which we'll need to pay for rental accommodation and the mortgage on the new build.
• Think about trees.  Removing large established trees is a nightmare.  Ensure that you have permission or will be able to remove trees early on, especially if you're going through the CDC approval route.  Alkira didn't explain to us that even if you have CDC approval, you cannot under that approval remove established large trees which are in the way.  Just because a tree is within your property footprint, this doesn't mean you can remove it.  You need to meet your local authorities' rules for removal which are often very strict.
• Add 50% to the base cost if you want an estimate of final build cost.  This is of course only if you want a fairly good quality finished home which is ready to move in to.  Prices quickly increase from the base 'all-included' prices.  Key drivers of our increases included i) Alkira's special offer upgrade package ($17k), ii) rock and tree removal costs ($25k), iii) statutory variations - water tanks etc ($18k), iv) extra dining room area ($23k), v) cornerless alfresco doors ($13k), vi) fireplace ($15k), vii) insulation upgrades ($6k), viii) flooring upgrades ($25k), ix) staircase upgrades ($5k), x) aircon and general electrical upgrades ($15k)
• Beware hidden costs.  Even if you're assured that there are no hidden costs, you might find there are some which pop up along the journey.  Ours included the following (which Alkira of course refused to pay even though they gave assurances that there were no hidden costs):
• $1k for reconnecting our gas supply after it was disconnected.  This was due to our property being a knock down and rebuild (something alkira say they specialise in, so unsure why they couldn't warn us of this cost or build it in to the contract)
• rock removal - seems crazy expensive to remove rock.  we added in a large provisional allowance for rock removal and alkira even tried to get us to reduce it a little as they thought it would be too much. Turns out it wasn't enough which resulted in increased costs
• anything to do with removing trees.  Also, be clear on what tree removal means... we paid someone to remove trees, only to find out the stumps which were left had to be 'ground out' at an extra cost before building could commence also.... and again this is something alkira failed to tell us about
• demolition costs aren't part of the contract prices usually
• driveways, and anything at all to do with gardens, deckings etc aren't in the contract price typically
• Add backs.  You'll receive 'allowances' for various items within your home.  They all make up part of the overall price and you'll struggle to get details out of the builders (or at least we did) but rest assured that the overall price you're paying was pulled out of thin air.  For example, our 'allowance' for carpets amounted to around $4k.  We selected better quality carpets at a cost of around $9k upstairs and we opted for wooden flooring downstairs.  Our tender came back originally without any credit for the flooring allowance of $4k included in the contract.  It was only after we queried a credit or contribution towards our flooring costs that the $4k credit was added back.  This happens many times over so query every upgrade variation you put through.
• Site Access.  This kinda makes sense but is at odds with what you always see on the TV shows about new home builds and of course is never explained to you during the sales process.... the contract states that you cannot access the site during the entire build process without the express consent of the site supervisor, and without him being there to accompany you.  From a safety perspective this makes sense.  However, we'd have thought if there are workmen on site, one of them could accompany you to show you around quickly if there's no material construction ongoing at the time.  The gap between perception and reality of the excitement of building a new home is bigger than we thought.  Luckily we can take some good pics from our property boundaries!
• Visualise 3D plans.  The reason you have to visualise them is that you won't get any.  Bizarre as it is that in our age of technology and decades after 3D imaging was commercialised, and of course considering the amount of $$$ you're spending, you won't get anything more than exterior view 2D plans.  Therefore, you really need to think about how your selections will look.  And don't expect much by way of advice on how things will look.  An example of an issue we came across was our selection of stacker doors out to our alfresco area.  Our alfresco area is basically one quarter of a large square lounge area.  The default plan was to have a column support, with sliding or bi-fold doors meeting up to the column.  Our issue is that we didn't want a big column in the middle of the room as we wanted it as open as possible.  We therefore paid extra for a beam, so that we didn't need a supporting column.  Our sliding stacker doors to the alfresco therefore meet, creating a great way of bringing the outdoors inside.  The issue is the height of the stacker doors.  Due to the size of the beam, the overall height of the stacker doors was substantially lowered, which creates the opposite effect we wanted.... i.e. it closes up the room instead of opening it as much as we'd liked.