unfortunately I came across this problem too. The biggest help to me was to download the viewer so i could figure out exactly what went where. As far as I know there isn't a really easy way to move the numbers so its less jumbled (since you need to line them up pretty much exactly).
If you are scoring/marking your lines by color so you know which way to fold them then my best advice is not to score those sections with any color, instead use something stiff that wont leave a mark which will help you be able to read the numbers a liiiiittle better.
If it's hard, when you complete it, the sense of achievment will be better!
Or, as Aeonyx said, just shrink the numbers
I'm starting my Pepakura today, so I made sure to shrink all the numbers and it's helped a lot!
Thanks very much Aeonyx!
And a very big...
GOOD LUCK raininggrunts!
Hope all turns out well!
I'll be keeping an eye on your profile, so please show us your updates regularly!