I don't know anything about a "standard" makefile.pl. I am relatively sure that each perl module should come with it's own makefile since each will have a dinstinct set of dependencies to resolve in order for the module to compile. You have two options I did not see mentioned in your posts.
Try using the CPAN shell to install the modules.
Try downloading the source for the modules in question and install those by hand. When doing this also make sure you read the readme files for any changes you may need to make to your paths before attempting to compile.