I think you did very good.
If the quarter panel is the only part that's rusted then imo it's worth fixing, but it's unlikely that's the only place that's rusted. It's not just surface rust either; you could probably stick your finger through that. I would expect to see rust in other areas, like in the trunk or the floor pan.
Getting a spare parts car is the smart option if you have the space to store it. The only replica parts (that I know of) are the ones on prelude3g.com, so if you break an obscure body part like a rear pillar molding or a heater controller, it's going to be a pain to get a replacement.I've owned my 88 2.0Si 4WS for nearly 20 years, and it's been occasionally stressful, but overall enjoyable and rewarding to work on over the years.. Unfortunately it's getting harder to find replacement parts for many of the unique bits on the 3g Prelude, so I had to buy a parts car this year.. This allowed me to fix a few things that have been bothering me over the years and has improved my driving experience greatly, so that's a great asset to have on hand.