So after finally getting the tranny back up with a new TOB, front cover seal, and oil seal, as well as putting in a whole new shifter bushing kit from Mazdatrix, I managed to start her up today, and she was idling very rough, and stalled a good few times before staying turned on, but idled incredibly low and rough (As kinda seen in vid 2), and then when going through the rev range, at about 1.5k RPM, it starts pulsing down to 1.3k RPMs and then back up, and then up to about 3.5k RPM the engine sounds very rough running (As seen in vid 1). The only things that have been changed that i could even think would effect that, would be the Reverse switch, or the exhaust leak at the downpipe. But I had an exhaust leak worse than it is now there before and this never happened, so I'm slightly doubting that. What are your guyses thoughts/guesses?

As well, there's a slight whining/hissing sound coming from my gauges that's not really audible in the vids. Would this be a bad speedo cable since it seems to match when I rev the engine?

 

So, update and some new symptoms.
Car idles rough when the AC is turned on, and then stalls. But when I push the clutch in, the RPMs spike, and either go to normal idle, or bounce between 1k and 1.3k.
Now, the thing is, with the AC off, it appears to idle just fine, but when I push the clutch in, the RPMs drop to about 500 or lower.
I am completely stumped at this point.

Video of said symptoms.