For anyone who cares, I was able to finally convert .bbl files into sword modules using the following process:

1. Rename the .bbl file to .mdb
2. Open with Access (if database locked with a password, google is your helper). Don't worry about any of the warnings you may get about old versions of Access
3. Open the "Bible" table
4. Export this file as an Excel 97-03 file
5. Use your excel-fu to format this file into a vpl file that looks like the example below. This file should have exactly 31102 files.
6. At this point I had to remove all bbl markup for italics or red text (using find/replace in my text editor) as I couldn't figure out how to change the markup into something Rapier would recognize
7. Save this formatted text as a text file (or .vpl, it doesnt matter)
8. Use the vpl2mod utility from http://crosswire.org/ftpmirror/pub/sword/utils/win32/
9. Run the vpl2mod utility using the following command line:
   vpl2mod <inputfile.vpl> <outputpath> 1 (that 1 at the end is important)
10. Create your own .conf file (see my example below)
11. And if all that works, you simply can place these files into the directory you've specified in Rapier. Ta-da!

It sounds like a lot of work, but actually following the above process only takes a couple minutes for each .bbl file you have. You could definitely use other sources for the text and follow the above instructions from step 8.

Sample .vpl file (more info)
Genesis 1:1 In the beginning God created the heavens and the earth.
Genesis 1:2 Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters.


Sample .conf file (more info)

[VERSION]
DataPath=./modules/texts/text/VERSION/
ModDrv=RawText
BlockType=BOOK
SourceType=GBF
Lang=en
GlobalOptionFilter=
SwordVersionDate=2006-10-25
Version=
Description=
About=
TextSource=
DistributionLicense=
LCSH=Bible. English.