First let me qualify my statements by saying that I have an '86 F-250 with a 6.9L. Have owned it since '87 and it's had a Banks kit on it since '87. I was also a Ford tech trained in the era when our trucks were built. I also have a bypass system on my truck. It was a Racor LFS 801, 7u absolute, but now it's a Racor ABS, currently with a 10u element in it as it breaks in from an overhaul (mostly head work but I went thru everything... less than 0.001" taper in cyls. at 140K miles and perfect lower end). I will work it down to a 5u filter (Racor offers the ABS in 3, 5 and 10u). Anyway, on to your stuff.
Yeah, where is the oil going? A quart every 2500-3000 miles (especially in freeway driving) is more or less normal for a 6.9L. That's what mine did even as a new engine. A quart every 1200.... not so good, especially considering only 65K miles (and I thought my 140K truck was low miles!!!)
First question, how long have you owned this truck? I ask because there is a notorious issue with 6.9L engines and oil consumption. Forgive me for redundancy if you already know this but it may help another down the road. Between the "Add" and "Full" marks is two quarts. If you keep adding oil to bring it up from the midway point to "Full" it will appear to use a lot of oil. If you add one quart when it reaches "Add" it will use substantially less. There is no windage tray on this engine, so I can only assume that the cause of increased consumption with the splashing that goes on.
One of the bad points of having a bypass system on is that it masks things in a UOA. I don't know what the efficiency ratings are for the NTZ filters, but if it's a fine filter, it's going to be altering the UOA readings somewhat. You need to relearn what's "normal." As was said above, between the oil consumption and the bypass filtration, the reality of your situation may be somewhat worse than it looks.
The sodium is alarming but not overly so considering you have no coolant loss. I would press on and test again. If you didn't change the oil, maybe do so as a "cleanout" and start fresh. That eliminates anything from your water pump work.
Finally, don't expect a big drop in wear metals in a normal UOA just because you have a bypass installed. The spectrographic analysis ignores particle above about 5u. The one UOA I got after I had the bypass on but before I overhauled the engine showed only slightly lower metals. I did, however, do a before and after contaminant analysis on the oil and there was a remarkable drop in that area in only 569 miles (see below). This was the LFS not the more efficient ABS.
LFS-802
Before oil had 1,700 miles on it.
Elapsed miles from install to oil test- 569
ISO Codes:
Before- 18/15
After- 16/13
Here's mine before the overhaul: