So after a long print the walls in the print begin to weaken and it appears they might not be printed at all. In the upside down picture you can see the weakness where the two pieces are separated. I'm wondering if perhaps reducing my speed and changing the extrusion size from .35 to .45 which is larger than the extruder itself. Thanks for any help and suggestions!
What you refer to as weak walls in fact are under-extruded walls. This can be caused by multiple sources, but, since the print recovers this most probably is caused by filament that is entangled on the spool (this causes more friction for the extruder and as such less flow, so under-extrusion; like as if the filament is being pulled back). Any other source that may induce extra friction is equally valid. E.g. kink in filament when using a Bowden configuration (long time extra friction in tube) or friction on the spool itself (I once had severe under-extrusion as the spindle of the spool caught a plastic bag which got wrapped around).
A filament tangle is one possibility, one alternative is that you are seeing a jam in the extruder. The trigger for a jam might be excessive retraction, heat soak or some other issue with the heat-break. Less likely, you might have an electrical problem which is position dependant.
The extrusion-related issues won't necessarily react in an 'obvious' way to any tweaks you make to the parameters (for example, slower might exacerbate heat-soak because the downward filament flow and thus cooling effect is lower).