Their egos were never merged. Nothing like that happened. What happened was Cloud, in his semi-catatonic state as they were escaping Nibelheim, adopted certain things from Zack. Cloud has a strong issue with failure... he failed to become a member of SOLDIER, and thus didnt identify himself to Tifa in Nibelheim because he was so ashamed. However, when he meets her in Midgar, he's convinced himself that things were otherwise, and told her he was in SOLDIER. He was, after all, found in Zack's uniform.

He doesnt know or remember Aerith. There's no evidence of such in their meeting, he has no idea who she is. It's Aerith that bases her feelings on Zack, stating that she'd had a boyfriend in SOLDIER.

Again, Cloud didnt 'absorb' any memories through experimentation. Not only were they in seperate tubes during the experiments, but there just isnt any evidence of memory absorption. Cloud has no memories that he shouldnt. He remembers the Nibelheim events because he was there. He doesnt remember SOLDIER training, Zack's parents, Aerith, or anything else.