Folding hard top that fits in the trunk is the way to go, it even gives you more room in the trunk.
Actually, this isn't true. In my personal experience, and despite the marketing hype, the three-piece hard top does take up more space in the trunk than the soft top - I've got all three tops (factory hard top, factory soft top, and the "trunk-top" three piece top), and, no matter how I stow the three piece top, I can get less stuff into the trunk than I can when I have the soft top in the trunk. Now, perhaps its just because I've had an RT/10 for almost 10 years and know how to fold the soft top to take up less space (very easy to do, just roll it up with some towels over the hard bits), but I can get in a overnight bag and car cover on top of the soft top, where I'm having great difficulties just getting the car cover in on top of the three pieces of the hard top - although there is more room on either side (in the side "pods") with the trunk top.
As far as how hard is it to get a soft top - are they still available via your local Dodge dealer? I replaced my Gen II's soft top in late 2004 and ordered it via the local Dodge parts counter, and they still had plenty of them available - granted, the price was significant - list was around $2k, and even with the local club discount, I still paid around $1700 for mine.
