This has just gotten more and more interesting.
IMO, the transfer method isn't the issue. Lightning, lasers, etc. As long as Lois gets the powers. Now, there's several different routes from there. Firstly, you'd have to determine when the transfer happened. Perhaps it happened when Clark was still a teenager, developing all of his powers when it happened. If the transfer takes away Clark's powers as well as giving them to Lois, then perhaps he hadn't even discovered the entirety of his powers yet. Lois receives them and discovers them as Clark would have, but unlike Clark, Lois hides her newfound powers from her fighting parents. Once she learns how to fly, she's out of there, goes off on her normal path, but with the continual development of her powers and she begins pondering her costume.
Clark, having lost his powers, goes on as normal, slowly regaining them (mostly his immune system/invulnerability and strength). He becomes a journalist, does *not* travel the world so extensively, but does end up working at the Daily Planet with none other than our Lois Lane. Lois has just decided to come out with her hero identity and feels stifled by her new partner. She eventually does reveal UltraWoman (or Wonder Woman, or whatever :p ), and Clark falls madly in love with her (not that he already didn't like Lois a lot). Of course, having never received all of his powers, he does not recognize her as having the same powers as him, though the possibility might have crossed his mind once or twice.
Clark chases UltraWoman stories the way canon Lois chased Superman ones. He slowly realizes he's gaining some new powers, and thinks that perhaps UW is the catalyst. He starts investigating her more closely, while Lois keeps throwing him off the trail. Then perhaps an event happens where Clark is forced to intervene and his powers come into play. He takes a page out of UW's playbook and creates a hero for himself, causing a rivalry between both the two heroes and the two reporters. Neither allow themselves to like each other because both like their superhero counterparts. And Superman and UltraWoman could end up having a secret affair and neither of them could know it was Lois/Clark they were really with!
Of course, they would both eventually realize that it was their reporting partner they were truly in love with, before discovering each others' secrets.
If you wanted Lois' powers to slowly fade, she could start losing them after meeting Clark, so that as his powers are on the rise, hers could be on the decline. Perhaps that's how Clark discovers her secret-- Lois gets sick/collapses in his presence (either as Lois herself and he questions her or as UW with CK and he takes off the mask/whatever and discovers her secret identity). Then he'd later tell her his own secret...
/sneaks up and takes that evil writer badge now
/
