I think your reading the handbook wrong mate. That's the the engine managment light (EML) the handbook may be saying to check the fuel and throttle body first before getting a diagnostic. It certainly isn't categorically one of those 2 things.
Your car is telling you there is a fault. You need a diagnostic to obtain the fault code which will tell where the problem is. It needs plugging into an OBD2 code reader to obtain the code.
Lexus will diagnose it for you for about £45. Or buy an OBD2 code reader from eBay and do it yourself. A list of OBD2 fault codes are here....
http://www.obd-codes.com/trouble_codes/
Codes staring with PO are generic for any car using OBD2.
A list of manufacturer specific codes is here...
These start with P1.
http://www.obd-codes.com/trouble_codes/lexus/
As you can see it could be many many things. As for driving the car, if it doesn't go into limp mode (can't go over 2500rpm) then the fault isn't going to damage your engine if you drive it, but you do need to sort this as you could be making things worse.