With all the theoretical designing done its time to move on to the practical design work. The next step involves the physical routing of the pipes, and keeping them as close as possible to the same length. This will really depend a ton of your vehicle and how much clearance you have to many different things. Of course, there are several different ways to approach this. I'll go over a couple.
1) Manually taking measurements and/or doing mock up work. This is not easy or quick, but you can take measurements and do some guess work as to how long each pipe needs to be. Possibly mocking something up with corrugated tubing (like smaller diameter dryer ducting), PVC tubing or something similar. Using a spreadsheet you can fairly easily add up pipe lengths with mandrel bends and see where you need to add/subtract length to make the primaries equal length.
2) Designing on a computer. This is also not easy for those who aren't familiar with the software, and even then it can be tricky to make sure things actually clear all obstacles around the header. You still need to take a lot of measurements when doing this. However, you can ensure that the header pipes are the same length and mess around a lot easier and quicker than mocking things up. Using this method it was quite easy and quick to figure out what tube should be on top/bottom, or left/right when they all come together. It also allows you to get exact tube cut lengths very easily for calculating how much tubing you need to order. Obviously, this is my preference. I use SolidWorks in my daily job so I'm pretty proficient using it. Another option would be
google sketchup which is free. The learning curve may be steep though.
This was the initial rough in of the header I made on lunch one way.
From that, I was pretty easily able to tweak the design to a fairly finalized model that you see below. Each runner's length is less than a 1/16" variance in length.
I was able to tweak the 45 degree bend length on the center runner to dial in the exact length I wanted.
I got lucky with the outer runners and they ended up being fairly close. To dial in their exact length, I adjusted the distance from the exhaust manifold flange to the first bend. You'll notice the right runner comes out farther than the left most runner.
You definitely want to keep things as simple as possible. The less bends the better. Not only for efficiency sake (less turns is less velocity lost), but its also cheaper (less mandrel bends to buy) and quicker to make with less complexity. I'm also not the worlds greatest welder and the less joints the better. I was really hoping to not have to put in the two 45 degree bends, and just use one 90 degree, but it just wouldn't work out. If you have the choice, a larger bend radius is also a better option as sharp turns steal more efficiency. Unfortunately, there isn't often multiple bend radius choices to be had.