An update:
I was able to get really good separation, nice crystals in the filter. I used small rosin press bags turned inside out and stuffed most of the way down the tube. I ended up trying fresher material and got a nice layer of terps which flowed without too much trouble.
Problems: Loss from transfer - seems unavoidable and has a large impact on the small runs i’d be doing.
Loading the carts went south real fast with the syringe failing, product cooling and solidifying and basically yakkety sacks should have been playing the whole time 
Solutions?
Remove the centrifuge entirely, just take live resin and slow heat it in a jar for like a day or two cap on - this would minimize loss from transferring terps which was my biggest source of loss and also took time.
Preheat carts and get a nice all glass syringe set up
@cyclopath - I wanted to thank you for your reply and other posts i’ve been checking out on the topic.
I def felt like giving up after my debacle. I also don’t want to get defeated by loading a damn cart.