I have some extremely old software (circa 1989, maybe older), that I need to get to run on a newer machine. Running the program itself is no big deal, it starts up and tries to communicate with an equally old piece of hardware and fails. The problem seems to be in the fact that the software is hardcoded to use a UART 16450 com port, and the hardware I have must be running 16550. So,my question is, is there anyway to emulate a 16450 com port, because the system that we originally used (AT&T 386)is failing.

You may try to run the application under an emulator and real DOS (that you must install from original floppies). A free x86 emulator is Bochs (http://bochs.sourceforge.net); it is quite complex to set up, but if you work hard eventually it operates fine (especially under DOS). If the effort is worthy, most depends on your goal as communication via Com port is still questionable (running under Microsoft host environments).