[brookn]

The spikes that are brown you can cut, cause they will not reflower. You cut the spike at the second or third node after the flowers drop, once it is brown won't flower again. Some people cut all the way off and some cut partially on the green spike, I am on the side of cutting the spike as far down as possible. The plant uses a lot of energy to flower and unless you are absolutely sure it is in great health (good roots, leaves, etc.) it is best to cut it back. The flowers that come from cutting the spike and reflowering usually are not as pretty as when it was first blooming.
Phals can be repotted at any time, but the blooms may blast, mine never have and I repot the minute I get one home, because I want to see the condition of the roots. I actually recently cut off a healthy spike with blooms (they weren't in great condition) because the plants roots were too iffy to me. I would rather save the plant to bloom another day than to kill it by letting it use all of it's energy blooming. It is customary though to repot after flowering.
The roots coming out of the top of the pot are normal. Some people call them aerial roots, but they are really just roots coming out of the pot. Some people say that the roots growing out of the pot is a sign that the medium is not making the plant happy or it just doesn't like it. I would get it out of the pot and inspect those roots. Let us know how that goes.