Deepwater52 , i almost have a same problem. Has a 2007 40 hp F40TLR..Bought a boat 4 weeks ago, yesterday I took it out first time. Had a little gas in it so I topped off with new and put stabil in it.
Motor starts , idle bad, shakes the motor, when i try to put it in gear dies off. Or even if I try to choke it.
After hours of research someone told me the jets are wrong size in carb by the factory! Because of their fuel efficiency...
Here is what he said:
"If you own a Yamaha 40hp you may experiencing acceleration issues and this is a factory defect . To solve the issue you must replace the jets. We are moving up from a #95 main jet to a #108 main jet then we are moving up from a #35 jet to a #45 jet. The part number for the jets that you need is 65W-14943-79-00 and 676-14948-05-00 and you need 3 of each jet. ********** is a good place to buy these jets"
So I will order it tonight.. Also I been told to replace the spark plugs to a NGK DPR6EA-9 !
I didn't mean to talk about my problem, and hijack your post, I believe we have a same issue. Also an other guy I found on facebook facing with a same problem.. Please let me know if you find out more. You welcome to call or text me as well. 713-884-552two
Here is couple of links:
http://www.*****************/boat-forum/showthread.php?220152-2008-Yamaha-F40TLR-4stroke-headache
https://www.youtube.com/watch?v=UZLTH94Yvnk&spfreload=5
Looks like some of my info edited by this forum, text me and I will send you the full links...