Take a look at what wooden shipbuilders do for long (longer than 12 inches) holes in timbers that have to be somewhat accurate. An example would be a tunnel for a prop shaft.
You don't say if you need to make through-holes, or auger to a specific depth. Modify these instructions to suit for that.
The key is to drill the hole more than once. Use a long, thinner bit, like 1/4inch or so, and setup plumbs or other references (such as lines along the length of the piece) to keep things true. Drill a pilot hole all the way through (or to the correct depth). It may help to have an assistant watching you to make sure you are true in multiple axes.
You will have to clear the chips often, and you may have to switch to using an extension at some point. Stop often and make sure you are running true.
If the pilot hole ends up in the right position at the other end (or depth), then you have a hole that one or more auger bits in increasing size will just follow. Some boat builders grind the threads off the point of the auger bit (if your auger has one) so the auger literally just falls into the pilot hole instead of trying to pull itself in. Clear chips often.
These bits come in very long lengths, or can be used with extensions. Since you will be clearing chips by hand very often there is no use using bits with flutes along the entire length. What we want is a carefully drilled pilot hole that you then auger out to specific diameter by following the pilot hole.