Wow -- 3 gals is a LOT of loss. And that's not just water loss, that's mostly wort loss which is very different.
I use the same setup: 2 10 gal round coolers and a keggle. I lose less than a quart in each vessel. Are you sure you can't improve on your system? Do you have a pickup tube on the keggle? Seriously, if I were losing 2 gals from my keggle every batch, I would just rack out of it and skip the tap.
Anyways, assuming you can improve on your losses, some level is inevitable. Losses to deadspace in the mash tun, boil kettle, and chiller (if applicable) all take away from your volume in the fermenter. So, work backwards. If you want 5 gals in the fermenter, first add your wort lost to the boil kettle, then from that figure out your evaporation loss to get your pre-boil volume, then add to that your mash tun loss. That should be the target volume.