1982- XS400 Runs poor (misses) at high revs in lower gears

If your engine runs fine in 5th at lower speeds use it, you will lower the revs and reduce fuel consumption and exhaust pollution.

The size of the crown wheel gear. Ford 9 inch is a strong diff used in V8 models. The 8.8 is slightly smaller but is still a good diff. The gear ratios will probably be different. Manual gearbox cars have different ratios to automatics. The higher the ratio, the faster takeoff you will have but lower terminal speed. At high speeds , the high ratio differential will cause high engine revs and poor fuel consumption. A low ratio will be mediocre takeoff but allows high top speeds and lower engine revs. (Good for fuel economy if you are mostly highway driving)

You could have either have the clutch not adjusted correctly or you could have glazing on the clutch discs or both. I would check for glazing on the clutch pack.If they seem glazed rub them on the cement a few times. The concrete will not harm anything but it will clear the glazing off of the clutch pack.

I’m happy to assist further over the phone at https://www.6ya.com/expert/robert_5bac37c3cb991fdb

at 2500 revs, there are several if not hundreds of possibilities. I recommend you have an OBD analysis done.

I would be looking at the coil,plug lead & plug any one or all of these may be breaking down under load it may also be a loose or worn main jet in the carby are you sure your not over revving it in the lower gears that is holding the gear a little bit to long before changing

no the code is most likely from a dpfe sensor for you egr system not the egr valve itself.a clogged fuel filter though might cause your low revs

when you cleaned the carb, did you remove the jets? Sounds to me like the high speed jet is plugged