Yaesu FT-991a with other software
This post is intended to be informational -- stuff I have searched the web for and did not find.
Baby step: Download and install the Yaesu comm port driver, hook up the N3FJP logbook to COM3 and life is good.
Next step: Download and install WSJT-X and JT-Alert. After a little fiddling with settings, life is still good. Logbook has to load last (JT-Alert can take care of this with its batch file feature), the logbook complains that Comm 3 is not available, OK that, and everything works.
Next step: Bought an SDRPlay RSPDX software defined receiver and loaded their SDRUno software. (https://www.sdrplay.com/) Amazing stuff, worked right out of the box. Added OmniRig, set a few parameters, pointed OmniRig to Comm 3 and SDRUno is working just fine controlling the Yaesu box and vice-versa. N3FJP log is not happy, however, because Comm 3 is already in use.
Current step: Internet wisdom says a comm port virtualizer might be the answer. Lots of them out there, oligopolistic market, it seems -- almost all priced at $129.95. Found "Virtual Serial Ports Emulator" by Eterlogic (http://www.eterlogic.com/Products.VSPE.html) priced at $24.95 with some good reviews. Downloaded and installed it. Set it up to virtually map a previously nonexistent COM10 to virtualize my old friend COM3. Pointed OmniRig and the logger both (!) to COM 10. Shazam! Everything works! Frequency and mode changes on SDRUno show up on the Yaesu and in the logbook. Changes from the Yaesu front panel show up in SDRUno and the logbook.
I am a computer guy by trade and will confess fearing that this multi-vendor contraption would soak up hours of my time and, in the end, fail to work. Instead I am sitting here amazed. Of course, YMMV, but life is like that.
I hope this helps someone.