http://www.futaba-rc.com/servos/futm0029.html

I cant find a sp48... do you mean s148?

the s148 is the "standard" servo and can be used on whatever you want for the lt-40.

I dont see a problem for any of the servos you have, its just one is older than the other.

as for channel assignment.

1 is ailerons
2 is elevator
3 is throttle
4 is rudder
5 is usually gear
6 is usually flaps
7 is usually second aileron

5,6,7,(8,9) can be used for whatever you want if your radio has that functionality.

there is no check valve on the tanks vent line... fuel inside the muffler wont hurt anything (unless you pour it out onto your carpet then you spouse/parent/SO might do damage )

good luck with the trainer.. you are getting help in flying it right?