Sounds like you need to be looking at configurations, you wouldn't have to split this into two or more files as a result.
As Bernie suggested, configurations is certainly something you should take a look at. Pack and Go may be another option. If you aren't familiar with it, it copies the top level assembly (or drawing), along with all it's dependent parts and sub-assemblies, to a new folder, without affecting the original. To do this, you open the top level assembly and go to File > Pack and Go. That will bring up a dialog box where you can browse to the location for the new files. You can also re-name the files as part of the process by double-clicking on the file name in the correct column. I'm at home now and don't have SW here, and can't remember the name of the column offhand, but it's not hard to figure out. There is also an option near the bottom of the dialog box to add a prefix or suffix to each file name. I highly recommend changing the name of any files that you'll be editing, and just to be on the safe side it's a good idea to re-name all of them. After completing the process, don't forget to close the original assembly and any other files that you have open before opening any of the new files and making changes. And yes, I learned that the hard way.
Thanks for the ideas. I did a pack and go and added a suffix to only the top level part. I quickly realized that wouldn't work. I made a list of all of the parts that needed to be changed and their parent assemblies, pack n go'd them with a suffix which worked out. All was going well until I had to move a gauge. All of its mates were deleted and it wasn't fixed but I couldn't move it. I had all of thesolidworks guys look at it. None could get it to budge. At that point anything I did effected the old model.
The reason for trying to not copy everything over is if a revision happens it needs to happen in all models.
Unfortunately i think I'll have to start from scratch with a new assembly. I'll definitely look at configurations when I get some free time.
It's possible that you may be running into some files with external references. Pack and Go should have updated the references, but without seeing your workflow, it's hard to tell.
I know it's a new job, but it sounds like you guys really need a PDM system. You can get by that way when working on fairly small assemblies, or with only a couple of people (we actually don't have PDM either....which I hate BTW...). As you can see, when bringing on new people it makes things difficult to keep track of everything, and eventually starts leading to more and more errors.
PDM is not something that can be thrown together in a few hours and expect it to run flawlessly, however, if you take the time to get everything set up correctly, it will make everything run much smoother.
Mates will not delete if you do pack and go, As Glenn said add suffix or prefix or you can change the required part number using select/replace option.
I believe revisions will not happen in all models if you do any changes in parent part. You may loose assembly references.
Unfortunately for you, somebody screwed up very badly on the initial installation of PDM Works. If it had been done well, the other guys there wouldn't be so down on it and you wouldn't be stuck trying to make a silk purse out of a sow's ear.
Configurations is the way to go in my mind. You can suppress your original gauge (instead of moving it) and have an alternate installation location, and suppress the original cap and insert the green cap. In fact, you can make configurations of your cap part with the different colors. Link display states to your configurations and name your configurations according to your naming conventions.