Let me see... The only perma anything I have seen is perma adol, but if you look in the God power thread you can see that the God of Youth is able to "curse" a SoA to stop growing in any stage. However, I don't know if that player is active and able to help with such a curse.
I have seen Gods customed as perma adols, and I think they cost the same as a regular adult. I don't know about regular customs.
For alt lines it depends on the colourist and on when you ask. Some colourists will finish all stages before sending out the litter, and in that case you can't ask them to change it later. For your own litters you can request what line set you want the cubs to end up as. You can't pick and mix for each and every cub, but it's possible to say that males grow to regular and females grow to alt, for example.
It's possible to ask for alternative lines for litter customs. In that case all cubs would grow up on the same line set, but the adult version could be different for some of the cubs. This would be something to write in the breeding form or custom form.
Some colourists have conversion threads (Look in this forum: http://www.gaiaonline.com/guilds/viewforum.php?f=155691) where you can request that your SoA is re-coloured on alt lines (or that they grow to the alt lines if they haven't finished growing yet). Post there if your colourist has one. If they don't you either need to find a conversion thread where a colourist offers to convert SoA they haven't coloured OR to wait for an opportunity to try to win a custom of your SoA on your desired lineset.