I know nothing about ebcdic, but according to
this, it has carriage return (CR = 0x0d (same as ascii of course)), newline (NL = 0x15), and linefeed (LF, 0x25).
I've no idea which of these characters ebcdic uses as an end-of-line marker, but whatever it is (I assume you know, or can figure it out from the files), you can easily convert it (or them) to the ascii newline that unix uses.
For example, if it uses the NL character (0x15), then
Code:
perl -i -wpe 's/\x15/\n/' <files>
should do it (note that this will do in-place replacement, so you might want to leave out the -i until you're sure it works...).
edit:
Oops, you'll probably need to add the g flag to make perl do a global replacement (i.e. 's/\x15/\n/g'), since there will probably be more than one per "line".