Yes, that was all just so Lois. If she'd first written "I love you" or even "Clark, it's me" or similar, the story would have seemed somewhat artificial. Instead, she responds to him as she always has-- "Clark Kent, you are SO dead" -- exactly as she would have if she were alive and he'd ticked her off.
And poor Clark doesn't immediately realize that it's Lois, even after the apology that follows the first message. Like Lois's initial disbelief in her present circumstances, he doesn't immediately think of ghosts.
You've effectively knocked out the obvious solution to this dilemma by having the Prof. distroy all his equipment and notes. And by following that scene with Clark's realization that a clone would always be just that, a copy of the original Lois, you've addressed one of the things that always bothered me a bit about the original TOGOM-- that Lois so easily accepted a clone of Clark.
So... like all the people who commented on your Lois & Clark/Samson challenge to Tank, IS there a way to fix this?
I like how the ghost thing is progressing without any seeming volition on Lois's part. With following Clark as Superman when he first flew off, she wished she could go too, then realized she was following him. With the shoe/lipstick, it was entirely accidental, wasn't it? Unless you take into consideration her strong emotion and the feeling that she wants to do something but can't do "one damn thing" about it.
Well, oh Queen of Angst and Cliffhangers, I am anxiously waiting for more. This isn't another Wendy/Tank challenge, is it?
~Toc