1 and 2 - do you think they are related to the problem?
Well, overloading your port pins and the supply can't be good!
3. pushing them gets them high why is that a problem?
It's bad engineering. While it may be (indeed is) the proper way to wire the lights in your house, connecting switches to the supply rail is a bad practice in digital circuits. Unfortunately, those writing the Arduino tutorials seemed to think they were indeed, wiring the lights in their house or else have some particularly unhelpful fantasy that they are making it "easier to understand" if the input goes HIGH when the switch is closed.
You do not want the 5 V line to be taken to any part of the circuit that it does not need; if nothing else this offers a point of failure if it is accidentally shorted to ground (and of course, complicates the wiring as the ground connection is virtually always present). If switches are wired to ground, then at worst, a short to ground will appear as a spurious actuation of the switch. The essential difference between switches used as inputs to logic systems and those in mains wiring is that these switches control next to no power and essentially harmless low voltages, whereas the primary purpose of those in your mains wiring is to render the circuit safe when turned off.
Microcontrollers such as the ATmegas are specifically designed to provide an internal pull-up to interface with switches or "open-collector" logic, which along with "negative logic", has been used from the beginning of digital logic design.
The only two reasons for providing an additional pull-up (which can be conveniently provided at the microcontroller end of the wiring where the +5 V line is already present) are to provide "wetting current" or to suppress the pick-up of interference on the wiring to switches at a distance.
4. why is that a problem?
5. ESP is working fine - I send and receive data with no problem
But feeding 5 V into a 3.3 V rated input - well, you may get away with it but this is a hot topic on the ESP8266 discussions - it may be bad for reliability. Put a diode with cathode to the Arduino and anode to the ESP input.
6. you're right - sorry - I only tested the movement sensor with only the USB cable connected.
I want to know with no LED, no ESP to talk to, how you know that it is in fact responding. What is your output device to tell you?
In short, you haven't posted your code!