Most FTP clients will do the right thing if you leave them in auto mode. However, auto mode usually means that they examine the file extension to know what to do. Some FTP clients are more clever about inspecting the file contents. Assuming you FTP'd the files one at a time, it's possible your FTP client didn't know what to do with a .pm file, and it transferred it in binary mode.
If you didn't use my "MT on DreamHost" install instructions, redo your install by following them. While they are written for MT 2.65, I've been told they work fine for MT 3.11.
If you want to try to fix your existing install, you could use dos2unix from a Linux shell prompt on all the Perl files. This is a lot of work and is fairly error prone, but it should undo the damage caused by transferring Perl files in binary mode, assuming that is the problem in the first place.
While this sounds like an FTP problem, it is strange that some stuff, like the login code, worked.