After talking with Elite about it, I sat down and I finally managed to get bots that safely have relativly stable random gene transfer.
Managed to find and overcome most of the problems, so far. One of the main ones is that veggies can pick up animal dna and become evil animal plant hybrids. Managed to prevent veggies from using the animal dna with epigenetics. The animals all store a value into 971. Then something like:
20 *.vel sub 2 div .up *971 777 div mult store
is used to prevent all these actions from occuring. A bit modified from what Elite mentioned, but the idea of preventing genes from activating in another bot really helped.
The second major was the reverse of this, animals acquiring plant dna. This led to the bizzare rapid reproduction I'd been seeing in the sims. I switched the plants dna to use basically the same repro gene the animals used and it was no longer a problem. I attempted epigen for plants, but many were dying off too fast to transfer the information(non-reproing plants are not fun).
Yet to be solved:
The worst problem left is caused by how relativly unintelligent the bots' genes are. Normally bots have one maybe two genes per action at most. Now imagine there are some 100 genes many exactly identical... The population would rise normally for awhile then begin to decline, apparently the additional gene costs tacked onto the gene transfer costs, were simply too much and eventually wiped them out. Fortunatly a simple "This location already has a value" dna strand should solve this one. :)
The second major problem, one I never thought of is that smaller genes replicate faster. This led the most useless of genes to gain an ever increasing percentage of the genome. To combat this I think a cyclic virus creator gene is in order, this way no one gene would gain an unfair advantage.
Huge genomes:
I'm planning to add in a "genome too big" deletion gene, keeping the genome down to a random 50 genes.
Alright, all I've got for tonight. Kind of makes me wonder though if real dna tries to keep its secrets to itself similarly. Makes sense that gene transfer might not be such a good thing between competing species.
I want to keep working on the dna some, I'll hopefully have a fully working bot in the next few days.