Honda city 1.5 manual has short gear ratios you can search the forums. I think gli is around 3.5k rpm at 120kph so 3800-4000 rpm sounds just right for honda city.
All the maintenance/repair items you mentioned other than clutch replacement has no effect on rpm to speed ratio for manual transmission.
Whereas for auto transmission, transmission slip and TC lockup are affected if some of these aren't within normal range.
If your clutch isn't working right you'd notice less acceleration compared to rpm increase
If acceleration and rpm change is linear (specially under load and on inclines) your clutch is working good.