Hi Mark, and Welcome to the Club.
I assume you have had the oil changed when you had the other gearbox work done --- it is supposed to be set for life but many owners have it replaced at around 70k miles.
The other thing I would try is to use the manual operation of the gears using the left side of the "J" gate by starting off in 1st gear and working up through the gears and then vice versa. That might give you a clue as to whether it is mechanical, electrical or hydraulic.
The engine warning light coming on and going off suggests something quite minor -- but it still needs checking out. Your local indie will probably do it for you, unless you know someone with an OBD2 code scanner. Jaguar charge about £70 to plug you into diagnostics ---- my mechanic either does it for nothing, unless it is a complicated set of codes it needs to read.
Let us know you get on.
Regards,
Peter.