BMW E90 LCI, after a long distance trip the engine started making a noise. Had the head fixed, then the car was not picking up RPMs, had the computer box changed to the original, car worked fine

Question edited for clarity, add MAKER!
Question moved to maker category.

BMW Flywheel Bolts = 100Nm or 74 ft-lbs of torque.
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Have you replace the fuel pump relay?

You can't reset the limp home mode, you must take it to the dealer and find out why the computer control is asking for limp to be engaged.

The first thing you need to check is for water contamination in the gearbox oil, if none try filling it with the correct procedure and reset adaptations, if there is water in the gearbox do not bother repairing it at a huge cost, they seldom get it right. Rather look for a good secondhand box that is the same make, the most common is the ZF6HP19

Can you wiggle the fan front to back when the engine is off? If so, check to see whether it is the water pump or the fan clutch and replace as required....

If pump is bad it will

It would not hurt to check it but the loss of oil and the loss of coolant are worrying. I would have a compression test done to check the head gasket and head. The tick may be compression gas escaping at the gasket. That would also account for coolant loss. Have a pressure test done on the cooling system to check for leaks. Towing a trailer ( I guess that it had a bit in it) over a long distance at speed ( probably 60 mph or better) places strain on a good engine but if the engine is on par or below then faults appear

The timing is set by the engine computer. It uses the crank position sensor. There is nothing you need to do unless you want to change the mapping of the engine.

Connect your old battery with another battery from another car (WHILE KEEPING ALL CABLES CONNECTED ON BOTH CARS) just user a bridge cable otherwise you'll need. a code to reactivate your BMW again. Try now to start your BMW engine. Now go to the nearest battery dealer to change the battery WHILE KEEPING YOUR ENGINE ON, otherwise you'll need a code to activate your BMW again :)

Good Luck!