Minecraft – How to transport animals over long distances

What you should do is make the water only one block deep, so that it all levels out. See the question that ZoogieZork posted. After that, you can dig as deep as you want and the currents shouldn't appear.

In general, here is a good technique for building rivers (top-down view):

█▒█▒█▒█▒█▒█▒█▒█... | █ = block
.█▒█▒█▒█▒█▒█▒█▒█.. | ▒ = water source
..█▒█▒█▒█▒█▒█▒█▒█. | . = empty block

First, you want to dig out a path for your river. Place alternating blocks and water sources along where your river is dug out so it looks like a checkerboard. Then, destroy all the blocks. Because there are water sources every other block, the space created by the blocks being destroyed will turn into source blocks themselves and create a nice and smooth river.

In your case, you would probably be able to build this pattern right up to one block before the lake. When you've destroyed all the blocks and the river is nice and smooth, you should be able to connect the lake and the river and the connection between them should level out.

If the biomes shifted it's probably due to a corrupted "seed" (just a long number) which seems to happen quite easily when the server crash. If you have an old save that still is ok you can get the correct seed from that save, and then edit your current save and set the correct seed.

It's really easy to read and set seeds with LolEdit. You just open the save in the editor and modify the seed field.

If you have explored new areas while the seed was corrupted you might also get problems with "sliced walls". Check my slighty longish answer in this thread for a solution to that.