1 cant stop the rain in tunnels
2 im not sure about using building parts as tunnels. some work and some dont. but also make sure thay are not too deep casue if u reach absolute height of 0 then you get fired into the air, that is until the .30 patch came out and now it kills u.
3 dunno why u would do but i like experimentation to i'll let u off
only thing u could do would be to put a wall ( metal or whatever ) where the invisible wall is so ppl wont think its weird ingame. the invizible wall should look ok from 1 direction but invisible from the other side.
4 nope, the water level stays constant throught the map. it could be a nice feature though if u told ppl to take their Lar-V, or try making the tunnel raise up at some point.
you will find many problems and limitations in the Mission EDitor. have a quick look at my 101 MED tips in the tutorials section to learn a few things. it may answer some questions u r likely to have