I think I have the stove running pretty good now.
After resealing every joint in the exhaust and the door, I think it is finally airtight. I'm not happy with the amount of silicone in the door gasket, but as long as it works for now, I'll take it.
I fired up the stove after the sealing and the draft fan sensor turned off, which means the loss in pressure was gone! I still had an issue with the pellets just piling up in the burn pot. After about 12 hours, the pot would be over flowing, and the bottom would be covered in "clinkers" or fused ash. This clogs the air holes which causes the flame to be lazy, as well as not allow ash to be trapped in the ash trap.
So, I also modified the draft fan thresholds a bit. The Factory setting is 100 for low, and 300 for high. I wish I knew what the units were, cfm maybe?
Anyway, after adjusting it to 170/315, the flame seems to be more stable, and the pellets are not piling up in the burn pot like they were on the default settings. If anything, I might need to turn it down just a bit; I think the flame may be too active. Although, my ash is nice and chocolate in color, a good sign the stove is running fairly efficient.
I'm sure that this will be an ongoing thing, but for now...I have heat :)