No worries about reviving an old thread. If you have questions and cannot find answers, then trust me, you are frustrated and will look for help anywhere! Been there, done that!
First, please understand that I don't know everything there is about the EWS system. I have a pretty decent understanding of it, but this is from reading different posts, manuals, inference, etc. Most knowledge, therefore, is theoretical. Programming new keys is absolutely practical because I have physically made three keys from scratch; so, in that area I feel comfortable answering absolutely, otherwise it is all subject to confirmation...
OK... So my understanding is that the EWS effectively needs to be registered with the car's main computer unit. At the very least, the EWS absolutely has the VIN number embedded within it (as do the transponders within the keys). If you think about it, this makes sense. It prevents someone from simply replacing an EWS with one of their own and "stealing" the car.... So, problem #1 for you is to register your EWS with the main computer. To do this, you will likely need something like the AK90. It has a hood that covers the EWS' microcontroller, and allows you to change things like the embedded VIN. It also allows you to register the different key transponders so, no, you don't need new keys (which, by the way, was misleading... at the most you'd only need new transponders but I've just discounted that).
So, there are a few things that need to be done (#3, #4 may not be required and are covered in a following paragraph):
1. you need to pair the EWS with the car computer (never done that, but I'm sure an AK90 will be involved)
2. you need to pair the keys with the EWS (done that, definitely requires an AK90, or similar device)
3. If you want to use the remote section of the key, you'll need to register the keys with the car computer (requires DIS, or similar, connected through the OBD port... done that)
4. You'll need to pair the remote with the car (the un/lock cycle stuff you'll read about on the net... won't work until #3 is done! Done that)
Now a few considerations... First, unless you have the barcode for the keys, you will need to run an algorithm to create the data needed when registering the remotes to the car (#3). HOWEVER, if you haven't replaced the car computer, which it sounds like you have not, then the remotes probably work fine now so #3 and #4 are probably moot points).
Second consideration.... This is an old car. Do you really want to go through the effort of installing a new EWS? Another option may be to simply disable the whole thing with one of the emulators sold on fleaBay. The disclaimer here is that I bought one and couldn't get it to work, but that is before I understood the nuances of needing DIS, etc. If I were to do it again, I think I might be able to get the emulator to work. Of course, at that point any key, regardless of the transponder (or if it even has one) will work, so it might be a theft concern. However, it is an old car and, ironically, I suspect that most of the time cars are just towed away anyhow!