Great progress. You are nearly to the realm of fine tuning. I have a few specific suggestion, but they do not address all your questions. Specifically, I still have a similar blob on layer changes and I'll be watching fro someone to suggest something that helps me too.
First Layer - In the initial photos, it looks pretty good. The top surface looks flat completely filled. The last photos of the more details part do look pretty bad. My first impression is that there may be a combination of too close to the bed (I know, your fixed that!), too much extrusion, and not sticking well to the glass plate. You may also have the hot end temperature too high. In my experience, I usually run the hot end just a few degrees above the low temperature rating of the filament.
Second layer - In picture 5, the second layer looks like it has ridging between the lines. This means excess plastic is being pushed around by the nozzle. If the layers below don;t have excess plastic (and they look good in this picture), I would suspect your extrusion rate is too high. You can reduce it in the web interface while printing, change the extruder steps per mm in your config.g, or (probably) make a setting change in your slicer. If you consistently change it in the printer interface or in the slicer, and with different reels of filament, you should probably adjust the steps per mm in config.g. I think it's best to tweak the extrudion % while looking at the second or third layer and not the first layer because the first layer can be affected by the z-offset. Once the higher layers look great, use baby steps to adjust the offset so the first layer looks great too.
Picture 6 - This looks to me like a classic example of a need for PA adjustment. PA (Pressure Advance) reduces the extrusion rate before the end of a line to compensate for oozing caused by pressure built up between the extruder motor and the hot end. You can adjust this live as your print builds up using M572 (see https://docs.duet3d.com/en/User_manual/Reference/Gcodes) . You can also probably do some clever stuff in the slicer to have it change the PA every 20 layers so you don't need to sit and watch it.
Blobbies and observations on the last photo. - There is some darkened filament stuck to the side of the part. In my experience, this is plastic that's been clinging to the nozzle and burning, then finally getting pulled off. The causes is often stringing that gets picked up when the nozzle runs past it, or anything else sticking up - like those blobs at the layer change, or the ridges from too much extrusion. And one you get some plastic built up on the nozzle, it becomes a stick place to grab more. I also notice that the blue boot looks like it might be dragging on the plastic surface and this could be sweeping up more crud to melt on the nozzle. I'd get that boot pushed on better (you might need to make the hole around the nozzle bigger). And I'd also look at the nozzle after every print and clean off any excess plastic you see while it's still hot. And also take the boot off occasionally and clean off the bottom of the hot end. I like these brushes because they are cheap and there's a box full ( https://www.amazon.com/Pack-Brass-Brush-Tooth-Brushes/dp/B07FN6K9J9). I keep some long and trim the bristles on some shorter with scissors. I like brass better than stainless because it's less likely to mar the hot end or nozzle. And don't let plastic build up on the brush or you'll be brushing on as much as you're brushing off.
Lastly - sorry this is so long. I like to use PrusaSlicer to get an idea for values of settings. I'll download the prusa config for a MK3.5 printer and see what it would use for all the settings. If mine are way off from that, I try to find a good reason, or test the Prusa value.
