That should be possible if you pipe from perl to the shell script, and back. I recommend taking a look at Bidirectional Communication with Another Process in perlipc, and at IPC::Open2.
in reply to Sub-Scripts Query
If your shell program prints out a prompt, then I guess you could just wait for the prompt via the Reader handle, and when it appears, resume your script. You can most likely even just send out the info to the shell script via a print via the Writer. It soon gets very hairy beyond those basics.
N.B. There's also the module Expect which serves to script other shell programs, but I've never used it and I'm quite sure it will not work well on Windows.