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I mentioned in my original post on dblue's Glitch that I've been able to run it in Logic 5.5 in Parallels Desktop. Of course that alone is a very small achievement. Here's the complete guide to processing only selected parts of a track (i.e. routed to a buss).

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First you'll need something that records audio off a buss. That could be an Audio Unit plugin (I could not find one that would record direct to disk. If you have one, let me know), or an entire application such as Soundflower. This example is based on Soundflower.

Disclaimer: This walkthrough assumes a fair amount of knowledge and understanding of Logic and digital audio as a whole. I won't be around for support if you can't grasp it. I will correct errors if you find any. I am not responsible if anything goes wrong. It worked for me. Period.

The steps:

1. Obviously, install Cycling 74's Soundflower. You will need to restart at this point so plan this step well in advance.
2. Launch Soundflowerbed and route Soundflower's 16ch output to the Built-in Output
3. Launch Logic and select Soundflower 16ch as your audio interface.
4. Open your original song. Place a Klopfgeist on an empty track and create a new region with a single note at 1 1 1 1, to mark the absolute beginning of your track. Do not skip this step.
5. Route desired tracks to mangle, to a buss of your choice. Route the output of the bus to Output 15-16. Do not place any effects on the buss, except a limiter if you need one.
6. Open your preferred sound recording application and set it up to record from Soundflower 16ch, input 15 and 16. Ensure that Soundflower outputs 15 and 16 are routed to None (no output, silent). Test your recording by creating a new file, hit Record, and play the Logic song. Anything routed to the buss should now be going straight to your sound app.
7. Create a new 24bit file. Rewind Logic back to the beginning. Hit Record on the sound app. Hit Play in Logic.
8. While the recording is underway, write down the tempo of your project. If you have a varying tempo track you'd need to replicate that in Logic/win.
9. Once your song is done, stop recording. Erase the portion of silence in the beginning, right up to the Klopfgeist hit. Zoom-in all the way and be as sample-accurate as possible. Save the file as wav.
10. Bounce the original song to a WAV file. Leave the Klopfgeist hit in. Open the file in your sound editor, delete the chunk of silence before the Klopfgeist hit (mine is about 2200 samples). Save file.
11. Copy both files (bounce and exported buss audio) to your Parallels shared folder.
12. Start up windows. Fire up Logic/win.
13. Logic /win runs stable with Plug-in delay compensation switched on, and sample-accuration automation on everything *except* plug-in parameters. Set that up
14. Add the two exported wav files to a Logic song as audio tracks. One is your tracking audio so you know where in the song you are. The other one (buss audio) you'll mangle.
15. Adjust the tempo. (replicate your tempo track if you have a varying tempo).
16. Place a Klopfgeist on an empty track and create a single note at 1 1 1 1. Do not skip this step.
17. Go to the environment and load up Glitch on the buss audio track. You can place as many effects before Glitch as you like. Do not place any effects after Glitch, except a limiter if you need one.
18. Arrange your clicks.
19. Once you're done, save your file
20. Solo the Glitch-ed track and Bounce to a wav. Logic/win skips at the beginning so begin your bounce at 0 4 4
21. Copy the resulting wave to your Parallels shared folder.
22. Open what you just copied in your sound editor. Delete silence at the beginning. Save the file.
23. Import that file in your original Logic /mac project.
24. Add effects and automation as desired.

The process is time consuming the first time. Provided you saved your file the next time it should be easy.

bars.mp3 - download result.