There was Chimeran technology under the planet the entire time, but how could there be if the Chimera were created by an alien virus?
There are hints that the Chimera have come to Earth before. Perhaps those early Chimera left it behind.
Outright confirmed in 2, when Daedalus and Malikov both refer to aliens burying their stuff here millions of years ago.
Where was the tower in New York dragging Earth to? Is there some sort of larger Chimera collective?
At some point there was. However, by the time the Resistance series takes place, it seems likely that they've been almost or entirely wiped out. The tower links back to the Chimeran homeworld, but in all likelihood there's nothing alive on it.
Why did some Chimera go feral?
The death of Daedalus fractured the Chimeran hivemeind. The more organized Chimera managed to stick together, but the less easily controlled strains broke off.
Where did all those alien plants come from?
Maybe the Chimeran virus mutates plants as well.
How did the humans rebuild New York City with only a tenth of the population?
They're probably not rebuilding everything.
Why was Capelli dishonorably discharged? Hale had turned into a Chimera, what else was Capelli going to do?
Changed or not, Hale had still accomplished a lot for the human side, and they were probably discouraged to see him go. Also Capelli was known to be a hothead so they might have thought he killed Hale needlessly when he could have been brought back and used as a source of information.
What confuses me is the Chimeran virus. How does it just make people not people anymore? Nathan Hale and Daedalus clearly had some ability to resist the hive mind and communicate with humans. Why can't anyone else still express their former selves? Just what, exactly, erases their former identities?
Probably neurological changes, if the Chimeran virus works as a form of viral genetic engineering it's probably inserting extra bits into their DNA as it works. If a human were resistant to it, though not immune, at least in theory the body cells would go first with the immune system working overtime to try to protect the core systems like the heart, brain, and lungs which the body will fail without. Of course unlike a normal viral agent the goal of the Chimeran virus is not to force cells to produce viruses instead of reproducing normally but to force them to produce Chimeran cells instead of human ones so when the immune system finally fails it doesn't result in death just infection of the brain that will slowly replace the human nervous tissue with Chimeran equivalent only retaining hardwired details or if they're lucky some memory storage that wasn't intentionally rewritten to make room for combat programming and such.