Hardware set up

I’m looking at getting an EX4100 empty and putting 2 3tb red drives in it. Raid 1 Is it a problem when i go to add 2 more drives to it or will it freak out when i go to add those drives to another Raid 1.

No it won’t freak out. It will ask you what you want to do with the new drives. Increase the capacity of the existing array and/or change the RAID type.

Awesome. That had been worrying me so i had been waiting on getting this till i could fill all 4 bays. Love the idea of it running Plex so i don’t have to have my tower on all the time. 3 gigs mirrored will do me for now but i know in a years time ill have to add another 3 gigs at least.

Plex uses a fair amount of resources on the EX series. You might be better off with the Pro (PRxxxx) or Business (Dlxxxx) series. More RAM and better CPU.
If you budget doesn’t stretch that far the EXxxxx series will work, just be prepared for the occasional transcoding delays.
I prefer the built in Twonky media server but I’m only using the DLNA server to send un-transcoded media to my “smart” TVs and tablets. It’s nowhere near as featured as Plex but it does run better on the EXxxxx.

I was planning on getting the 4 gig ram chip to expand the ram of the EX series with it anyways. I have found the recommend ram chip for $15 so that would expand it to 6 gigs of ram. With the dual core i should be ok to stream the MKV files i have transcoded my movies into or should i transcode them into a different codex for easier transcoding with the dual core.

It depends on the devices you are streaming to. If they can play whatever file format is inside the MKV container they won’t need transcoding.