[Turning off mods crashes the server?]

Perhaps Multiverse is still loading the old world as well. Check to see if the old world was removed from worlds.yml or whatever file Multiverse uses to configure the worlds available.

[Add treecaptiator to Tekkit SSP?]

You may be able to just drop the treecapitator zip into the tekkit mods folder: %appdata%\.techniclauncher\tekkit\mods\

If it works,(I just tried it and it works fine) it should have no effect on SMP. Keep in mind you need to use the treecapitator version for Minecraft 1.1.

Edit: It looks like the last version made by DaftPVF was for Minecraft 1.1 and can be found on this page.

[Server stopping at random]

This log looks the same as my test server logs, which run fine and don't crash. Line 206 of the log has the time it took to start "2012-04-08 04:31:55 [iNFO] Done (0.913s)! For help, type "help" or "?"". There are some EE, RP2 and Railcraft messages that appear after this, but that happens on my working server.

["Took to long to log in" on my own server]

I've been getting similar connection issues. I think that this is symptomatic of Minecraft.net server issues. If login validation with Mojang times out then this error occurs. Perhaps there is a high number of logins this holiday weekend?