I'm considering purchasing a 1990 Samurai. I'm aware that it's EFI vs Carb, but are there any other major differences between these and the mid to late 80s samurai's? Just don't want to run into issues ordering body panels/parts/etc. I see most places only say up through '88 on models?

All I can say is there are some changes between the early Samurais and the 1988.5+ Samurais in the US. I think there is different gearing and the dash is different but I could not tell you more.