Well, I'm still struggling with that mission. I just did 4 attempts, and still nothing. i'm going to call it a night on SA-- it's just a video game and it's starting to piss me off.
With the jetpack, it is possible to get somewhat of an advantage, but all the overhangs and crane things make maneuvering difficult. Also, the train seems to speed up in the tunnel, so even with the jetpack going as fast as it will go it's hard to keep up.
I also tried killing the train engineer-- you can shoot through the windshield like you can in a car. (I did this before driving into the marker in unity station in hopes that the train wouldn't move-- it didn't work. The engineer apparently respawns when you drive into the marker and the train still moves.
)
Once, due to a glitch, the train stopped and I was able to get up there. You can kill the three guys towards the front, but the guy in the back is immune to weapon damage (he gets snagged on that first red crane thing and that is the only way he can die-- kind of stupid because you're so busy trying to stay with the train you never notice otherwise. )
I managed to get back on the train after avoiding the red crane, and there just isn't enough time to kill all 3 remaining guys before you come to an overpass that you can't duck under. terrible, just terrible.
After playing San Andreas for awhile, it just feels like I'm playing beta software. There are tons of annoying little glitches and missions like this should have been adjusted in development or at least during the PC port-- nothing should be this hard.
A glitch like this ruined my last savegame-- I made it to angel pine (after beating the Badlands mission) and at this point you are supposed to receive a phone call from Cesar Vialpando before the game will continue. However, for some reason, that phone call never happens, so since no new missions are unlocked, the most I can do is wander the map. I had to start over fresh.