0. Oh no, Wakasa Rumi, who is currently in disguise and under an alias, looks slightly different from Elena Miyano! Her possibly fake age is also different! But wait there's more - her name is Wakasa Rumi, not Elena Miyano, so they can't be the same person! /sarcasm
Stop assuming we know any information about Elena's strength and intelligence in solving cases. There is indeed a falsehood when you say that we know 100% that they are different from Rumi's.
And yes, Elena is supposed to be dead. Can't see how this negates a theory claiming that she faked her death.
1. There is no evidence of a love affair between Kohji and Wakasa. Rumi keeps the Shogi piece because it is somehow important to the organization (as evidenced by Wakita bringing it up).
2. Simply put, different voice actors (obviously not going to give them the same voice actor). Alternatively we have vocal variation, pitch variation, etc. She's not trying to mimic someone else's voice, just making her voice sound slightly different. There would also be an 18 year difference between past-Elena's voice and Wakasa-Elena's voice.
3. She knew her research was backed by the Carasuma Group who turned out to be a super bad organization, Kohji left the dying message CARASUMA, she knows the true purpose of APTX 4869, etc. etc. There are many ways for her to make the conclusion that "Carasuma" is associated with "a sly black conspirator".
4. Ah yes, the classic family pattern of Atsushi the biochemist, Elena the biochemist, Shiho the biochemist, and Akemi the ... banker robber. Elena has a 30 year advantage (if she is alive) and you are equating her intelligence to that of Haibara's.
5. Why would Amanda appoint only a singular bodyguard Wakasa Rumi? Was she that confident, but Rumi still failed her? This issue doesn't really seem specific to Elena being Wakasa.
6. Yes, I've already explained this. By my theory Elena Miyano's hair darkened during her time in the organization (either naturally or artificially). So her hair was dark black near the end of her time in the organization. Then her hair would of course be black at the time of Kohji's murder scene.
Your argument in trying to prove Wakasa is 100% not Elena hinges entirely on assumptions. I have admittedly made a few assumptions but my goal is only to show that there is a strong possibility for Wakasa to be Elena, not to definitively prove 100% that Wakasa is indeed Elena.
It would be much more convincing if you instead proposed an alternate theory as to who Wakasa Rumi is that better fits all the information we've been given and back it up with strong evidence. Then this argument can be more than a back-and-forth where you say "A is false because I believe B" and I say "Well A could still be true because B could be false", and then you say "Well that's false because I believe B", etc.