ahoeben

Use an infill pattern instead of modeling the grid.

Oh, sure, go ahead, blame the innocent plugin 😉 I don't see how that plugin could cause CuraEngine to fail... It mostly just toggles the Cura preference to auto-slice. Pausing and unpausing effectively results in restarting the slice, which CuraEngine should be able to do just fine.

Just know that that version is 9 years old.

The major blocks are 10 mm; if you zoom in you will see that there is a finer grid at 1 mm. No, you can not easily change this in the software.

There's also the "Custom printjob naming" plugin from the Marketplace, which will let you customize the prefix (or add a postfix) based on settings.

CuraEngine does not actually use the Nozzle Size setting, but instead it uses the Line Width setting and some other more specific line width settings. In part this is a leftover from a time where most Ultimaker profiles would use a line width that was 7/8th of the nozzle size (so a 0.4 mm nozzle would print with a 0.35 mm line width). The optimal Line Width to print with is affected by the nozzle diameter. But you can print fatter and thinner lines than the nozzle diameter. The line width and the layer height determine how much material needs to be extruded. The material diameter is used to convert that to the amount of E-steps. The flow parameter is just a multiplier to adjust for slight miscalibrations and material slipping. For printers that have a nozzle size dropdown, you are actually not just affecting the nozzle size, but you are loading an entire settings profile that could have many other setting changes (such as printing speed, material temperatures, etc).

Wire printing was removed in Cura 5.4. According to the release notes, it was "broken and barely used". You could try Cura 5.3 (https://github.com/Ultimaker/Cura/releases/tag/5.3.0), or let us know what you mean by "it is no longer working" and perhaps we can help you to (also) get that version to work again.

The extrusions will have relatively low number number of steppermotor steps, so there is less precision in how much material gets extruded on a move. There is no hard limit of what is "ok" and what is not, but with a lower layer height, you get less precision in how much material gets extruded, so (theoretically) you get very small under- and over extrusions along the print due to rounding. This is even more a problem for "relative" extrusion mode, since the rounding of steps happens at each move instead of over a full print.

Cura tries to protect your printer against cold extrusion. Cura tries to see if there is anything in your start gcode that heats up your extruder(s), and bed. If not, it will insert a heatup sequence on its own. Cura does not know about your PRINT_START macro. The logic is here: https://github.com/Ultimaker/Cura/blob/4.4/plugins/CuraEngineBackend/StartSliceJob.py#L428 Cura looks for the text "{material_print_temperature}", "{material_print_temperature_layer_0}", "{default_material_print_temperature}", "{material_initial_print_temperature}", "{material_final_print_temperature}" or "{material_standby_temperature}" in the start gcode to check if the start gcode contains extruder heating commands (so it does not actually care if you use M104 or M109 or not). Cura looks for the text "{material_bed_temperature}" or "{material_bed_temperature_layer_0}" in the start gcode to check if the start gcode contains bed heating command (so it does not actually care if you use M140 or M190 or not).

I have never printed a benchy myself. I went to 3dbenchy.com, and downloaded the 3d benchy hosted on Thingiverse.com. 3D Builder (by Microsoft, ships with Windows) agrees with Mesh Tools that that model is "invalidly defined" (which is what 3D Builder calls non-watertight). Just that a model is printed a lot does not mean that it is a perfect model. But let's not focus too much in this topic on what is and what isn't watertight.

Is Cura itself, or the Mesh Tools plugin telling you that it isn't?

There is no such thing as Ultimaker Cura 4.1.3. There is Ultimaker 4.13 (which I think you have), which is newer than 4.6, 4.7 or 4.8. You can download 4.13.1 (the latest from the 4.x releases) here: https://github.com/Ultimaker/Cura/releases/tag/4.13.1 Other releases can all be found here: https://github.com/Ultimaker/Cura/releases/ (You will have to scroll)

You don't have to turn off the plugin; you could just turn off the warning if it is annoying you. Though it is there for a reason.

The one in your screenshot is shown by the MeshTools plugin. If you want, you can turn them off in the settings for MeshTools (see Extensions -> Mesh Tools -> Settings...). MeshTools checks if a mesh is watertight by making sure every edge ("line between two vertices") of the mesh is included in exactly two faces.

The message means that Cura thinks there is nothing printable on the buildplate. Is your model on the buildplate, or has Cura placed it off the buildplate? Could you share a screenshot?