Thanks guys, we've taken notes on everything posted. Here is what we have for 1.04:
-New Reference Data
-New Convert Data
-List of Changed Files
You can grab the 1.04 reference data, a new convert data a list of all the changed files here: https://stardock.cachefly.net/SinsModPackage1.04.zip. You probably won't be able to use these files correctly without the associated exe but it will allow you to get going on your conversions.
-Entity name lookup is now case insensitve.
-I can't release the symbol file for security reasons but there are new options to enable error messages. This can be turned on by modders in the user.setting file to simplify tracking down errors instead of mysteriously crashing. (i.e You can use ShowErrors TRUE to get more info).
-For those of you who may have missed it, instructions on XSI and how to get Sins meshes in the game from scratch are included in the Modding Documentation here: https://www.sinsofasolarempire.com/Modding_Documentation.zip
-You should never have to convertdata every file by hand. We use python scripts to automate things like this (very easy) and the batch control method (a bit more cryptic) listed earlier in this thread is good as well depending on what you are doing.
Judging by the posts here, perhaps one of the best things I can do is explain how mod development should operate. You need to setup an environment and toolset very similiar to game development.
First, you need scripts to automate stuff (i.e ConvertData). I recommend Python and there are plenty of beginner examples out there that run through a bunch of directories/files and applies a program to them.
You need comparison tools. Once you look at my zip file look at the report of files. I use a program that compares the entire Sins 1.04 directory with the Sins 1.03 directory. I turn on full binary comparison and turn off time stamps (there are lots of other options). Then I tweak a bunch of easy filters to give me just the files that differ or are/aren't included across the two versions. I can also easily click each of those files to see the exact differences and it gives me the option to manually or automaticaly merge them among a variety of other tricks. I then spit out a report of the differences for you guys. This is how you should be upgrading mods. As a test, I pretended to update my "modded" files to the 1.04 format and using this method it took about 5 minutes. Depending on the size of your mod I really can't see it taking more than 20-30 minutes. The program I use and I very strongly recommend it is called "Beyond Compare". Its free for 30 days (and very reasonably priced for its power) so give it a shot. I've been looking around and I can't find one that is more suited to game development. We will be ordering copies for the whole company soon given how much the demo has improved my workflow (we previously used a weaker, free program that I won't rag on but it wasn't as nearly as good).
Finally, anyone working in modding or software development needs to use some form of source control. It would take me a very long time to list all the advantages but the basic idea is you have a program that stores versions of completed files. You then request from the program to modify a file and when you are done you submit it back to the program who tracks the entire history/evolution of the file(s). At any point you can do a "difference" between an earlier version and the one you are working on so you can see what you changed or you can revert back to an early non-bugged version etc. There are plenty of free source control programs out there including CVS and Subversion.
Edit: Oh and source control makes it much easier for multiple people to work on the project 
Well that's just a quick overview. I may write up a more detailed basic mod development tutorial using free tools if that is something you guys feel you would actually try out. I can see from the various comments in this thread and all over the modding section that most people would benefit a fair bit. The basics of proper development aren't too difficult but they yield so much.
P.S Since there seems to be a lot of interest in merging mods: the things I'm talking about should make this sort of thing relatively painless.