*High Quality* BD should run extremely similar to PetroD. Some notice it quiets the engine a tiny amount. Performance differences should be well within 10%. BD exhaust smells A LOT better.
BD *may* have a slightly higher gel point than winter grade PD but I think those low wintertime temperatures have passed in your area by this time of year.
Not likely the cause of your problems, unless the BD was low quality or waterlogged.
Warning: 100% BD can prematurely degrade non-BD compatible fuel system rubber (fuel hoses, older IP seals), causing them to soften and weep.
OTOH, BD inherently has higher lubrication qualities than current ULSD, potentially increasing IP and injector lifespans (assuming IP seals are BD resistant).
Previously you stated you thought eyeballing the camshaft timing was close enough and wouldn't cause performance problems. ("The cam timing could be a little bit wrong but I don't think that could effect the engine too much.") I don't have direct experience with this so will not overtly dispute that but--- Why would the factory make a special tool and additionally specify loading the adjustment 0.2mm to one side if eyeballing was close enough? Why should they complicate the process?
Also: "Adjusted the valves to pretty much exactly to what the book says..."
What is "pretty much exactly to what the book says?" Either followed the method and specs or not? If not, what did you do different?
Did you measure clearance with the head fully torqued to the block or before?
Hot or cold?
Not meaning to run you around but there must be something amiss. We agree that it
should be running better, not worse, after a new head, light rework, new headgasket, timing, etc., no?
Let's verify and clarify where you are at now. Apparently the performance and driveability are continuing to incrementally improve? Acceptable smoke? Only remaining issue is low RPM stumble? Please clarify if I misread.