ok bear with me, this is going to be a long reply to answer each of your queries individually. 
(needed to split it into 3 posts because of the number of quotes.)
from your parts list, seeing how you don't really need a hard drive for storage (320GB not really worth bothering with in my opinion.) i'd save myself about $150 by getting the 4690 (not the k, k means it can be overclocked easily because it has an unlocked multiplier), getting a h97 motherboard and not z97 one, not getting the hard drive and then putting some of those savings towards getting a 500GB ssd instead of the 250GB drive. saving you about $100 total so far.
if you want i can visit the micro center site and source a build from there for you if you like.
actually if you stick to using the pcpartpicker site for all components then take your final list to your micro center in person even if they don't usually hold stock or deal with a certain manufacturer for the part you have on the list you may find they will buy it in special for you anyway, if not they will at least recommend a part that is compatible that they do stock.
Bluetooth I could get after unless the board has it. I hope I chose a board that gives ample on board audio and graphics. My current Del XPS 8300 has NVidia video and audio cards so i don't know if not getting cards is a mistake.
no the board doesn't have blutooth capabilities so would need to buy a dongle later and unless your an audiophile then the onboard sound will be good enough so no need for an extra sound card, as to a video card always worth while in my opinion but not really needed if you don't play games, and you've already said you don't need one.
The CPU I chose has its own cooler
good so no need to buy one.
I'd like hyper threading but I have done without and it is not crucial. Maybe this processor has it.
no, i5's do not have hyperthreading so that cpu doesn't have it.
I don't think I need WiFi as my router generates a WiFi signal and I am connected to the ISP by an ethernet cable.
right wifi is needed by both devices pc and router IF you are going to connect wirelessly, you said your not and are using an ethernet cable so no you don't need wifi capabilities.
Network confuses me. Do I need an NIC or does the Ethernet do that?
same thing really, so yes the nic/ethernet is built into the motherboard so you don't need to buy a separate device.
Is PCI for the graphics card?
pci is an old type of connection (slot) built into the motherboard used for communication with the cpu, doubt you'll have one, the newer pci-e slot though, yes it will have one, usually used for graphics cards but can install other devices into them. eg i have a tv card in one of my pci-e slots.
The PSU seems to have enough watts but I did not know if that is the only consideration.
what your really looking at besides the "watts" is the amps on it's 12v rail, but don't worry to much about it and just use the site linked to in other topic to check if your choice of psu is a good one, like i said stick to about 500 watts 80+ bronze and you'll have more than enough power for your system.
I thought b/c I only show 38 GB of a TB used on my C: currently, a 250 GB SSD would be enough along with a HHD.
like i said earlier i wouldn't bother getting a 250GB ssd and 320GB hard drive, and just get a 500GB ssd seeing how you don't need the storage. personally i wouldn't buy a storage drive less than 1TB just not cost effective otherwise in my opinion.
Besides these 4 I could either make a list here to bring, or go to Micro center and ask for help selecting whatever else I need.
you need a psu, ram, dvd-rw drive, and case minimum to complete the build.
I don't know if i have to paste the CPU.
no the thermal paste will already be applied to the heat sink, but it might be worth buying a small amount in case you need to remove and replace the heatsink, you will also need some cleaning fluid to clean both the contact areas before reapplying the new paste.
