You said, " For the improvements that were unit specific, and not for the entire property, I just don't think it is fair to apply those independently to each sides cost basis, because the both units are sold together at the end, with no way of knowing how the overall sale price was effected by one sides renovations."
No, it is absolutely fair to treat them differently. The sale of your personal side is straight-up capital gain or even exclusion of capital gain.
The rental side is a combination of capital gain (possibly) and ordinary income. There are calculations made on Form 4797 that determine what amounts are treated in what ways. These are two separate properties. One is personal, subject to certain rules, one is rental, subject to completely different rules. The fact that they are sharing walls is irrelevant.
