How to speed up a game of Empire Builder?
One dis-recommendation: don't lower the amount of money for the win condition.  The game advances through phases from initial building (limited range) to networking to running those few big deals that are finally possible late in the game.  By reducing the win condition you'd be cutting out that last phase and that can be a lot of fun.

Tested recommendations:


Setup: alphabetize the goods if you haven't already so "banking" is fast.  This is huge, as otherwise looking through a bunch of different goods with tiny pictures is a pain.
Check BoardGameGeek for player aids.  It can be hard to study the map to plan your move without getting in the way of the active player, but a copy of the map can help (not so much with detailed track planning, but with "where the heck is $city on this map?" planning.  Granted that should be less of a problem on a map of one's own country, but it still helps.)  Similarly, make sure everybody has the "where does this good come from?" card for planning.
Increase starting money by 20 and add one more round of initial building.  I've tried this a few times with Iron Dragon with experienced players.  The effect was to increase the value of those first early runs, thus jump-starting track building.  It didn't make a huge difference in elapsed time (maybe 10%), but it did cut down on the early feelings of angst and futility that can come with unfortunate cards.)


Untested ideas:


Allow each player some small number of "I hate this card" redraws, without the cost of a full-round flush.  I would limit this to the early stages of the game -- maybe up to three uses while your money remains under 100.  The idea is to soften those "aw, crap, I guess I could go there for 10" runs that don't really help you except to flush the card.
If time is being lost because inexperienced players can't plan their turns in advance, consider some scheme for parallel turns.  Play is largely non-interactive, after all.  Maybe a player and the one opposite him at the table can go at the same time so long as they aren't competing for the same pip, goods token, etc?  (If so, turn order wins.)


I don't think any of these would damage the spirit of the game, unlike, say, removing some calamities from the deck would.