If you choose to upgrade them both to 4*, regardless of what level they are at when you choose to upgrade them, their damage will be the exact same, both being 4* Lv 1 Ascended Caliburs.
Ideally, you'll want to upgrade 3* to 4* gear as soon as you're able to; at Lv 5.
Nope. They're the same. Tempered Calibur and Ascended Calibur are separate and the only way the former can affect how the latter turns out is if you have a UV that you transfer.