Mis-fire codes don't store for some reason. I learned this when my CAT was clogged on my 01 Camaro. To get it to throw the code have them hook in the scanner, put it in drive, and power brake it. I know it'* dangerous but it should make it start acting up. At least for my car it did.

I did install the fuel filter and I ran some fuel cleaner.

Considering this is it safe to assume it was a misfire since there are no codes stored? Im sorry but im not familiar with power braking, do you mean gas and brake at the same time while in drive?

I'd say it'* safe to assume that. And yes, power braking is gas and brake at same time.

Just a little update, I was able to get the code pulled and it was a 0306, cylinder 6 misfire. I checked the plug and wire in 6 and they both fine. I tested the coil and the coil came up fine as well. I checked and tested the rest of the plugs and coils too.
So I'm guessing that the injectors are next but my question is, is there any way to check there flow or to see if they are still functioning without removing them??

While your engine is running, you could disconnect the #6 injector connector and see if the engine runs differently.

That wouldn't hurt or damage anything in the engine? I am definitely going to try that.

Nope, your only disconnecting it for a couple seconds. NOTE: This may illuminate your service engine soon light.