I haven't taken it, either. To compare flights, try www.skyscanner.com. The motion of the train doesn't bother me much but starting and stopping could cause more of a jolt as well as noise from brakes and whistles (bring ear plugs). This is the train schedule through May 28, 2018:
Madrid-Chamartin dep 21:43
Avila
arr 23:09
dep 23:11
Medina del Campo
arr 23:55
dep 00:11
Salamanca
arr 00:57
dep 01:00
Ciudad Rodrigo
arr 02:06
dep 02:07
Fuentes de Onoro
arr 02:28
dep 02:30
Vilar Formoso
arr 01:35
dep 01:50
Guarda(P)
arr 02:21
dep 02:23
Celorico da Beira
arr 02:48
dep 02:49
Mangualde
arr 03:24
dep 03:25
Santa Comba Dao
arr 03:55
dep 03:56
Coimbra-B
arr 04:52
dep 04:54
Pombal
arr 05:21
dep 05:22
Caxarias
arr 05:42
dep 05:43
Entroncamento
arr 06:05
dep 06:06
Lisboa Oriente
arr 07:20
dep 07:22
Lisboa Santa Apolonia
arr 07:30