There are rail-joiners available on the DLS as track-objects. I can't remember who made them though.
The bridge is fine; deer get used to things like that, besides, trains don't pass that often. We have a herd of deer that frequent my bird feeder to steal the feed out of the feeder and to eat the cracked corn my dad puts out for the ducks, turkeys and for the deer. They cross the street when they can and hang out in the driveway and don't care if we're around. We don't approach them and leave them alone while they eat.
In real life, I think it's in Utah or Wyoming, there's a highway overpass meant strictly for wildlife. There's a camera placed nearby showing the animal traffic crossing the bridge including bobcats, antelope, and other critters. Given the amount of traffic below, we would think the animals would shy away from the bridge, but nope they cross anyway and a lot safer too than playing in traffic.