First off, I never said -6 was higher than -1. I just said we could artificially give it precedence.
Second, what I'm thinking doesn't involve any kind of artificial pairing of genes, or anything along those lines.
You'd have DNA threads, each being a chromosome. Each has a beginning and an end. These threads then all activate simoltaneously. If you have multiple copies of the same chromosome, then you have multiplie copies of the same chromosome. Woop de do.
From this simple system, diploid and Xploid DNA could naturally develop. Sexual reproduction would simply be combining the DNA of two haploid cells (which is where real sexual reproduction came from).
So, aside from non-linear DNA all we'd have to add is a way for DNA to be divided into threads, and for a way for cells to combine their DNA (maybe some kind of fusing, the opposite of reproducing).
Also, we'd have to add a time delay for DNA reproduction based on the length of the DNA. Real organisms will reproduce through meiosis if they are stressed because it's much faster (you don't have to reproduce any chromosomes, you just split the diploid DNA and you're good to go.)
Last, we have to add a way for chromosomes to become associated with each other. Similar to the centromeres in real chromosomes. Real chromosomes do this with a long series of repeating patterns that somehow keep the two chromosomes together.
As I said before Zelos, genes will just learn to have the highest strength in your system. That doesn't help us at all.