All versions of the game seem to use the same file formats now (the encoding is not important, AFAIK). There are just a couple of things to watch out for:
1) The original game only has five user-accessible style sets, and each is shared by two or three races. In DA/TA, each race has its own style so the Sn_ prefixes on the ship files will most likely not match up. You'll need to change the number there in order for it to appear uder the race you expect it to. This is probably what you're running into right now.
2) Between DA and TA a lot of parts have gotten updated, higher quality models. A number of these models may not match up internally as to the order of the hardpoints, etc., and that can result in mangled designs if you try to copy them straight over. This isn't so easy to fix as the first issue. Most people who wanted to do this badly enough ended up copying all the old models back in from DA, and re-adding the improved ones as additional options. Note though that doing this will break all the base templates for similar reasons as the DA designs broke, so you'll want to copy the DA templates over too.
