Reducing the number of genes should help. Also, I think store commands cost you energy every cycle, whether or not they are activated.
Store commands cost .04 nrg per cycle, and genes cost .004 per cycle, so try to reduce the store commands and number of genes. It can save quite a lot if you've got lots of them.
For instance, you could replace the whole reproduction gene with this one line, which you could put in gene one:
*.nrg 5000 sub 0 floor sgn 50 mult .repro store
That'll get rid of one gene, saving 0.04 energy per cycle(not much, but it adds up)
You can also make things like movement more efficient, which would reduce costs dramatically.
Another thing to consider is the use of inc/dec, which use no energy at all.