Actually I'm not sure if Johnny died or not around MK3. According to various sources his death might have only been in the movie. Also if I understand it correctly, Liu Kang's soul may not have reuinted with his body until his ending in MKD. I think until then someone else (Shang Tsung?) was in control. Also Scorpion wasn't killed at the end of MKDA, instead he escaped and found his way to the Elder Gods to become their champion.
Liu Kang (Bio for Deception)
The sorcerer Shang Tsung had killed me and consumed my soul. I
remained trapped within his being, tormented by his evil, along with
many other victims of his vampiric soul drain. Through Shang Tsung's
eyes, we witnessed the battle with Raiden, who sacrificed himself to
stop Onaga. Raiden's blast destroyed Shang Tsung and our souls were
free to ascend into the heavens. I remained in Outworld, however, to
aid my friends in the fight against the Dragon King.
Liu Kang Bio 2
Why someone would desecrate my grave and reanimate my body, I
cannot say. Somehow my corpse retains my knowledge of martial arts,
and has killed many innocents. Though I am not the perpetrator of
these slayings, I cannot help but feel responsible for the brutality
committed by my corporal form. The battle between mind and body has
I think you are right about the whole soul reuniting with body thing though.
Scorpion's ending (Deadly Alliance)
The hunt for Quan Chi had led Scorpion to the palace of Shang Tsung. Scorpion entered the palace through a hidden passage. As he made his way to the lower levels, he was discovered by the two Oni he had previously encountered while in the Netherealm. Shang Tsung had secretly allied with Moloch and Drahmin as a backup defense against Quan Chi. The two Oni had been hidden in an underground chamber and were periodically fed mortals to keep them satisfied. Scorpion fought well, but he was overwhelmed by Moloch and Drahmin.
Although they could not consume the Ninja Spectre, they devised another means for eliminating foe that would satisfy their cruel nature. The Oni brought Scorpion before the portal to the heavens that Shang Tsung had tapped as a source of limitless souls. They hurled him into the Soulnado and his hellspawn body was ripped to pieces by the purity of that realm.
Midway pulled a Deus Ex with this one
According to a faqs in Gamefaqs
Cage died in Mortal Kombat Trilogy (though whether Trilogy's storyline is cannoncal is easily debatable)