Intellectual Ventures is a patent troll. They shouldn't even exist. Laws must ban those organizations that merely collect patents and waiting to sue people. Creativity killing machines!!
Not so long ago, I was pretty much in your situation, except that I didn't have a PhD. I was moving into a software engineering role from a DevOps role. I was initially flunking a number of interviews at pretty much the same companies you have mentioned. My advice as most, Practice and Patience while solving problems. Practice talking through a problem in particular. The interviewer is waiting with a hint in hand, which you can always use to get a direction in which to solve the problem. Getting this hint 100% of the time from the interviewer is 100% fine.
As for study, I highly recommend the index page of this book, Elements of Programming Interviews, as a reference. It contains a catalogue of questions, whose complexity exceeds that of CTCI or PIE. Here are the links.
Apache Thrift http://thrift.apache.org/docs/ - A feature rich RPC framework with documentation that completely sucks. The docs page has evolved from "coming soon" over the last few months. You would have to dig deep into the library headers to find hidden "easter egg features".
Reading Lawrence of Arabia by Scott Anderson - So far I have got a vivid picture of the events leading up to World War I and how opportunistic the Standard Oil Company were. This is a long book. So, I plan to interleave my reading with either "The Map Thief" by Michael Blanding or "Diary of a nobody" by George Grossmith.