Ouch, cutting up the boxes on those late plastic tray games? Well, luckily if you have manuals for those games they are technically complete by most standards. For whatever reason I've found that most collectors don't care about the boxes when it comes to TG games.
You might already be aware but if you contact Sparky (a member here and pcenginefx forums) you can get custom spine stickers that look awesome. It's a great way to make those games that came with plastic trays look just like all the other games.