If all you have is FTP access, you probably won't be able to do things like make the file (perl executable) executable as far a linux goes.

Strictly speaking, on Linux, an executable doesn't need to be executable :)  You can always run it directly via the dynamic loader. If you don't believe it, try the following:

Copy the perl binary to some temp directory

$ cp `which perl` /tmp
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Remove the executable bit

$ chmod -x /tmp/perl
$ ls -l /tmp/perl
-rw-r--r-- 1 ab ab 1061700 Apr 20 00:47 /tmp/perl
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Now, if you try to run it normally, you'd of course get

$ /tmp/perl -v
bash: /tmp/perl: Permission denied
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but if you use the dynamic loader, it works without a hitch

$ /lib/ld-linux.so.2 /tmp/perl -v

This is perl, v5.8.8 built for x86_64-linux-thread-multi
(...)
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Also depending on the setup, you could potentially not have access to your rc files (bashrc, cshrc, bash_profile) and would thus be unable to set environment variables needed

You don't necessarily need to. If you have mod_env available, you can conveniently set them from your apache config (e.g. for the CGI directory in question):

SetEnv LD_LIBRARY_PATH /path/to/private/shared/libs
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This even works with .htaccess files, so you don't need write access to the main httpd.conf. Also, as I tried to point out, it's probably not even a good idea to set LD_LIBRARY_PATH system-wide from some rc file (too many side effects if you mess with important libs on that scale...).