Thanks Squid! I followed your steps after I installed the hapticless bottom lockbar and I was able to get the transitions back in place.
Here is what I did:
1. download desired transition from OP
2. extract it to sdcard (I put mine in /mnt/sdcard/ROMs/transitions)
3. grab Ninjamorph Free from the Market (and Astro if you don't already have it)
4. run Ninjamorph
5. select New Project
6. browse to /system/framework
7. select framework-res.apk
8. wait for extract to complete
9. press Home key, open Astro
10. in Astro, browse to where you extracted the transition folder
(e.g. /mnt/sdcard/ROMs/transitions/flipandfly)
11. long press on anim folder, select Edit, then Copy
12. in Astro, browse to /mnt/sdcard/AndroidThemes/workspace/framework-resapk/res
13. select Paste and overwrite the anim folder
14. press Home key, launch Ninjamorph
15. get back to main Ninjamorph screen, select Finish Project
16. select framework-resapk and confirm all changes & zipalign & reboot
I did have a weird issue with Ninjamorph where I would launch it again after copying the files in Astro but Ninjamorph would not be at the main screen, it would still show me the file/folder list. I just used the "Back" soft key until I was at the root directory, one more "Back" would cause Ninjamorph to FC. Then when launching Ninjamorph again I would be at the main screen and could then select Finish Project. Kinda sloppy but I didn't see a way to get Ninjamorph back to it's main screen.