In the first sentence, the will is optional.
In the second sentence is fine as it is.
The third sentence is better written as:
The train which will be refilled tomorrow morning will leave at 9 pm.
"leaves" is not commonly used and may not even be proper. See: http://www.verbix.com/webverbix/English/leave.html
You said "The train which is refilled tomorrow...". "is refilled" is confusing, as "is" is present tense and "refilled" is past tense. In addition, "tomorow" is in the future. I think you meant that the train will be refilled tomorrow. A wordier way of saying this is:
The train which is going to be refilled tomorrow morning will leave at 9 pm.
but I don't recommend that, as it is unnecessary wordy.
Following the link's pluperfect future tense:
The train which is going to be refilled tomorrow morning will have left at 9 pm.
but this is not necessary.