First thing coming to mind is: check ground/earth straps for engine, batteries, and at/under the left and right kickpanels.
But, we could probably narrow it down better...
Let's see:
1 The car is still drivable
2 Does not go into top gear and gear changes are rough
3 The power is reduced (sounds like the Eng./Gear ECU has detected a fault condition)
4 The CEL is on, and the speedo is "off".
5 A 2006. The car is nearly new. What's the milage?
a) Any other instruments or anything else not working?
b) Did you get/do a Trouble Code reading? (Two ways, Toyota Tester or OBD2 reader; or manual reading the blinking-code of the CEL. (I think a 2006 HDJ must be obd2 compliant?)
c) Any water-crossing or similar?
d) Any sign of leaking windscreen? (Often appears first as Engine ECU problems because water would drip down onto the ECU. Did you ever change the windscreen? (Takes an experienced pro to get it right)