1 - Tactics for lizard command structure?
2 - In short, tactics for saurus and skinks?
3 - salamanders worth it?
4 - Roles for Kroxigor and temple guard?
5 - Stegadon, worth it?
1 - For the command structure. As Guthwine says, try to keep your main units within a "diviine guidance" bubble. I'd have these as saurus units (includes temple guard and kroxigors if in the list) aim this block towards an area you wish to control.... could be determined by the scenario, could be a hill you want to conquer...
2 - saurus have the reptilian rule, skinks don't. As mentioned above i'd put saurus near your slaan mage, and skinks flanking using dense terrain as cover. Try and hassle your opponent and slow him down.
3 - expensive troops for the lizardmen army. You already have some expensive but elite troops. They seem okay, salamanders remind me a bit of dark elf crossbowmen, because you want to get within 15cm to shoot them, and they are 75 pnts for 3 stands. Ideally you need 3 stands. I'd try them out, they could be effective at disrupting your enemy.
4 - i'd put these with the saurus. Elite infantry versions, similar role
5 - same as 3, they are expensive. You break point will be very low with one of these. I wouldn't take a stegadon in a 2k game or lower game. Try to aim around break point 10 for a 2k army, or 9.
I like the flyers you can have in your list. I'd use the skink heroes that are commanding your flank troops (cold ones and skinks) to home back the terradons, then land behind your enemy, shooting at them. Then charge in a unit of cold ones, this should be enough to auto destroy almost anything in one round of combat. If your command check fails keep a skink shaman nearby to leap into the unit, and cast "wings in the jungle"
(if you can confuse your enemy with shooting, then charge using that spell it'd be great)