I think I have the solution (now that I've learned quite a lot about the format of a PCF file and the bugs in PENG).

Take each of you IR hex signals. The sample you posted above was:
0000 0009 0000 0023 0014 0069 0014 0032 0014 00c3 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 07d0

Change the frequency to something that doesn't trigger the severe bugs in PENG. I changed the 9 to 90 getting
0000 0090 0000 0023 0014 0069 0014 0032 0014 00c3 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 0069 0014 07d0

Paste that in to PENG.
Save the PCF file.
Use a zip program, such as WinZip or Wiz to open up the PCF file.
Extract the xml file (unless you're particularly good at navigating the primitive text editor that may be built into your zip program).
Open the xml file in a text editor (such as WordPad).
Find the IR codes. The one shown above will look like this:

32 0 f 6c 4 7f 7c 14 69 32 c3 3f 5f bc 12 32 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 c1 37
(you can search for the text "code>" and the IR code comes right after that.)

The sixth value in the IR code is the frequency. 7f in the TSU3000 corresponds to 90 in Pronto Hex. Change that to 8. So you get

32 0 f 6c 4 8 7c 14 69 32 c3 3f 5f bc 12 32 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 c1 37

Save the corrected XML file, then update it into the PCF file (how to do that depends on which zip program you're using).

Open the PCF file and load it to the remote.
You can open the IR signal and look at the Pronto hex and see that it is roughly right (PENG does only a poor job of translating its internal format to Pronto hex, vs. the horrid job it does translating Pronto Hex to its internal format). If you do so, don't press OK, and/or don't save the PCF file. Even if you just look at the Pronto Hex and don't edit it, PENG translates back corrupting the signal.

I hope your device isn't too picky about the exact timing because the above only gets things close. With all of PENG's rounding errors I can't compute its actual time unit, so I don't know for sure how much the timing drifts when you use a value like 0090 for the wavelength (frequency) word in the Pronto hex, so I don't know what tweaking is called for other than changing the frequency.