Is the 'not a first printer' warning actually that serious?

I built a dual-headed machine as my first serious build and finished it, but I'll be honest about where the pain acutally was. The mechanical stuff was fine because that's what all the guides cover. The config was where I lost weekends. So if your frame is square and both heads are mounted, you've done the hard physical part already. Don't box it up.

The two Z motors refusing to level is almost certainly not crooked lead screws. With two Z steppers Klipper can run them from seperate stepper_z1 style sections, but the usual way is one motor per side with a shared Z section and the gantry forced square by endstops. What you want is two independent Z endstops, one on each side, and Klipper's Z tilt or quad gantry style leveling routine doing the squaring for you every home. If your config only has one endstop, one motor will always be slightly ahead of the other and it'll look exactly like what you're describing. Get both sides homing independently first, then worry about wether the screws are straight. For the two heads, resist the urge to write it from scratch. Find a working config for a similar dual toolhead machine and read it line by line. The swap logic is basicly a gcode macro that parks the idle head, turns off its heater and fan, then activates the other tool's extruder and heater. Once you see one written out it stops being scary.

And on the wires, label everything before you plug it in the second time. Sounds dumb but it saved me hours.

It's not a weekend of frustration, it's more like two or three weekends of frustration. Same thing though.

Gonna push back on the two or three weekends estimate. My first machine was nowhere near as fancy as this one and it took me most of a summer to get prints I'd actually show someone. First builds have a way of hiding problems behind each other, you fix the leveling and suddenly the bed mesh is garbage, fix that and the temps drift. If OP is already at the config stage with a square frame, maybe they're quicker than me, but I'd budget a month of evenings and be happy if it beats that.

I went through this same wall on a two-motor Z setup a couple years back and the thing that finally cracked it for me was a cheap machinist square from the hardware store. I kept blaming my config when in reality one lead screw was seated a hair off in its mount. Took the square, checked each screw against the rail, shimmed one with a washer, and suddenly the motors agreed. So before you touch any more settings, verify the hardware is actually square. If it is, then it's all software from there, wich is annoying but fixable.

Honestly I'd unplug the second toolhead for a bit and get one head moving and printing first. I did that on my two-head build and it made everthing way less overwhelming. You can always add the second extruder back into the config once the machine does the basic stuff without complaining. The idle head doesn't need to exist for the printer to work, so don't let it sit there psyching you out. Also keep a copy of the config before every big change, renaming the file each time. When something breaks at 1am you'll want to flip back two versions instead of staring at the mess wondering what you touched.

So I did check the mounts with a square, and it turned out one of the lead screws was seating slightly off. That solved the major leveling issue, which was huge. But now I'm facing a new problem with the motion settings. The X and Y feel smooth, but the speed limits are causing wierd stalls during the print.