Hi i have a few suggestions for you. Sorry for the messy nature of the post, writing isn't one of my strengths. This might not all be 100% accurate either, although it will give you a few ideas you can try.
I have mentioned the mapsize issue in another thread. When the game loads your level up, during the function LevelSetup() it checks to see that neighbouring planets are connected. If it finds any that are not connected, it adjust the SendDistance value of the planet to "connect" it.
The global Globals.G.MaxAsteroidNeighbourDist=() determines the maximum distance between planets the game will allow. The globals Globals.Asteroids.MinSendDistance and Globals.Asteroids.MaxSendDistance do exactly what you think they do. If these globals are not set high enough for the game to make all the planets have at least one neighbour, the game will crash. So you could set these to a rediculously high values like 100'000, if you do that however, you'd have to manually set all the send distance values of each planet in function LevelLogic().
I haven't seen your map, but if you are using stable orbits then this should be very easy (for you at least, i couldn't do it). You'd only need to add a bit of code that lists the planets in order of the radius of their orbit, compares them with each other and sets appropriate SendDistance values.
Just to note, the planets don't need to connect up in function LevelLogic(), it only applies to setup.
I've made a map with a range of -300'000,300'000 on the x and y axis, i'm unsure as to what the maximum possible is.
As for the seedlings not settling down, all ten seedlings must be able to land in the exact same place before a tree will sprout. I had the same issue as you when i doubled the speed of the seedlings when i was experimenting with a faster paced eufloria. I'm assuming the fact that your planets are moving is creating a similar issue. You could try increasing/decreasing the seedlings speed. There are three globals for seedling speed... Globals.Agents.MaximumSpeed=(), Globals.Agents.MinimumSpeed=(), Globals.Agents.SpeedPowerRule=(). The last value works logarithmically, if you plotted the planet "speed" (Energy,strength,speed) value next to the seedlings actual speed on a graph it would be a curve. The last value merely determined how curved the graph would be (i think?!?)
You could also try changing the turn speed of the seedlings, with better turning they may be able to settle easier. Globals.Agents.TurnRate=().
If neither of those two suggestions work to a satisfactory level, you could try slowing down the orbits of the planets.
As for the seedling planting behaviour, the problem is probably similar to above. The roots will only stop growing once they hit a predetermined point, i'd assume if the planet was moving too fast, they'd never hit that point. Globals.Structures.RootSpeed=() Determines the speed at which the roots grow. The default value is 40, the lower the value the slower they grow. I'd suggest you try increasing this value.
With the 2000 foot tall tree's, i imagine it's a similar problem as above. Because the planets are moving, it might be preventing the tree's from hitting a predetermined point, so they just keep growing. Globals.Structures.LevelTime1 to Globals.Structures.LevelTime4 determine how fast a tree grows between each level. By selecting lower figures (to make the tree grow faster), you might fix this problem.
Lastly the planets being unclickable happened on my two levels i made. If you have seedlings on a planet that does not belong to you (no flowers) and the planet is not connected to any other planet you own, then you cannot select that planet. You can get around this with a piece of code that checks all the planets to see if they have flowers. For those without flowers, it checks if you have seedlings there, and then sets the planet as being owned by you. You might consider comparing the players seedlings, to the AI's seedlings on a planet with the code giving ownership of the planet to whomever has more seedlings.
One problem this would cause, is it would allow the player to travel the entire map, without having any flowers, as long as they left one seedling on each planet. To get around this, you could set the SendDistance values of planets to be dependant on flowers being present.