I feel wheelsets are most important components for a endurance ride of this magnitude, Broken spokes can ruin your dream at the same time sluggish wheelsets can make ur ride painfully slow in final 300-400km, The OEM wheelsets are baisc stuff even on high end bikes. A faster , stronger and wheelet always help, am looking forward to upgrading wheelsets (faster, stronger and reliable, alloy only), presently using basic Shimano RS 11, Please advice.
Weight makes a difference despite what others may tell you. Everytime you change speed in an upwards direction you'll notice it. With regards to buying new wheels, it all depends on what you want them to do (go really fast/be bomb proof/ be easily serviceable/ have easily available replacement parts). Generally speaking some of the racing orientated top-end factory wheelsets with huge proprietory spokes will be stiff as anything and great fun. They can also be amazingly strong. However, they can have a limited lifespan due to manufacturers only supporting them with spares for a number of years. Compare that with conventional rims and spokes that will be around for years and can be bought and delivered in 24 hours.
It also depends on your budget. Are you loaded? Do you want to buy a £600 factory wheelset and tear arse to Edimburgh? Or do you want a handbuilt set for £300 that are 300g heavier, but have rims that can be replaced easily and a hub that will last and last?
It also depends on you. Are you graced with extra lard which will put extra stress on your equipment? Do you ride with souplesse on rough road surfaces or do you hit the potholes like a sack of spuds? Will you be carrying the bare minimum, or will you do a mattc and carry a whole workshop in your saddlebag because your bike is so poorly maintained that you are likely to need it?
All things to think about. Unless you are light, fit, loaded and on a racing machine then handbuilts are probably the way to go. There are loads of good builders around. You wont go wrong with Hewitt, DCR wheels etc. Id be tempted to give David at DCR a ring and tell him what you need them for and get a range of options.