Cool idea. Here are ways to solve some of the problems mentioned:
1. Chromosomes should be defined by DNA commands.
chromostart
blah-blah
chromoend
Within a single chromosome the stack is used as before - allows inter-gene communication. Each new chromosome resets the stack. To make your old files run in new version, simply add chromostart in the beginning and chromoend at the end - most of the bots should be just fine this way.
2. Allow single-chromosome genomes. After all, not all genomes are diploid. Poliploidy is not necessary, it does not add much anyway.
3. All pairing up that is needed is just to place paired chromosomes one after another. During sexual reproduction, take odd chromosomes from mother, even from father (just like sexrepro works now). This actually makes tetraploidy possible (or any other even-number-ploidies).
Comment:
Nums, organisms don't go through meiosis just because it is faster :) There are always better reasons :) But we can make meiosis possible, should not be hard.