The communication specs for your gun should be publicly available. Almost everything I have ever dealt with that interfaced in that way have very simple interfaces that can even be controlled via a regular terminal emulator. So you could always try that.
Also if the source code is available it could probably be ported to Pocket PC pretty easily. In fact, it should be a simple program to just write from scratch. eVB would be a good candidate for that type of program.
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