First Orchid (Possible Stem Rot Problem)

[Orchid2017]

Hi everyone!

I just got my first orchid, a mini phalaenopsis, I can tell that this will be a lifetime hobby, so I wanted to join a good message board to learn as much as I can

So far, I have a few concerns, so I wanted to get your thoughts on a couple things I noticed:

-First, two leaves have a few discolored/indented areas on them. A local greenhouse thought it might be sunburn.
-Second, (and most concerning) was some blackening and spotting at the base of the stem where the roots connect.

During re-potting, about 30% of the interior roots were dead, there was mold in the center, and most of the other roots had dark spots, but were still green and firm. The orchid does have two large healthy-looking aerial roots though.
After that, I doused the roots with hydrogen peroxide, put a little cinnamon on the black sections, and re-potted it into a bark mix.
I also left the two flower spikes alone since they're in good shape.

What do you think? Will she be ok? And should I consider clipping the flowers to focus on roots/leaf growth?

On the bright side, the crown/rest of the plant looks healthy!

Thanks in advance!