Seems you have it figured out, but i will say that in my experience, messing around with any of the road leveling/raising features tends to be very time and patience intensive. Also results in very large files, and often hangs the software or crashes my PC. For the issue of a bridge not meeting the road neatly i would agree that shifting the road and bridge somewhere else is a much better idea. I tend to look at the terrain in 3D view and find a spot where the ground either side of the water is at a gentle slope and the same height on both sides. Also, when replacing an unsatisfactory bridge, i would recommend against 'placing' bridges, and find it best to:
1) delete the bridge
2) move the roads to a better location (you will have a gap in the road now)
3) rejoin/merge the roads
4) in the edit menu at top of page select 'bridge roads'
5) take a look in the 3D world and repeat if needed
And another thing! The terrain in the map editor doesnt always look how it does in the sce editor, which may be different again to what you see when actually playing the scenario.
So in the case of a bridge and road not being neat; if its only a minor misalignment that doesnt look like it will stop units from driving over the bridge (vehicles are surprisingly tolerant of big chunks of concrete with reo-bar poking out of it, it looks worse than it is usually)- dont worry about it.