How to Decipher Lego Building Instructions Filenames?
After emailing back and forth with LEGO, I think I have an acceptable answer:

Example:

BI 3005/48 - 7594 V 110 2/2 - Download size: 5.94 Mb
^   ^   ^      ^   ^     ^                   ^
1   2   3      4   5     6                   7



Stands for Building Instructions
A number for internal usage by different LEGO teams.  


You'll see that many different sets share this number, and all the numbers are fairly close (generally in the early 3000's).  My guess is that it has something to do with whoever drafted and finalized the instruction manual.

This number shows the number of pages in the manual.


When the number is show x+y, that means x building pages, and y instructional pages (e.g. what to do with bricks, or what bags are needed).

This is the set number.
This number refers to the page format of the instruction manual.


V29 means ISO A4 paper format.
V39 means letter paper format.
Other Vs (like 110, 140, etc) are different file formats.  LEGO said "those are the types of versions throughout our country that we ship to".  I'm guessing that they are related to the official formats for the manuals that are included with the kits.

The booklet number:  x/y means x booklet number out of y booklets.
The file size of the instruction in megabytes (not megabits, as it would seem to imply).