Trouble finding gear/echo??

Hey new to the forum and to the 2nd generation truck (coming from an 86 Toyota P/U w/500,000 miles) I understand these trucks make a lot of engine noises-- injectors/emission controls/valves and I have a moderate background in auto mechanics but just wanted to get some input--
About a month ago I bought an 05 Double Cab 4.0 w/Auto with 77k on it (love it and huge difference over the 86 ) but noticed recently that its occasionally (only happened twice now, but boggles me) having issues finding a gear-when slowly accelerating in a straight line- it will hit 3-3500 rpms in second gear, then dropping super low in another gear and bouncing back to normal rpm/correct gear--?? I read these trucks ecu's "learn your driving habits" so maybe its confused? haha

Secondly-- Occasionally under acceleration at other times then above, I can hear what sounds like the timing chain rubbing on the case coming from the front end- (22rs could be famous for this when you had to much slop in the guides and chain itself)-- It does have an aftermarket cold air on it but did it before installing as well...

Thank you for any input, just want to get to know this truck like my old one-

 

the auto has a great reputation as not having any problems. it is a decorated and successful hunter though.

and as far as engine noise, I wouldn't worry about the chain(s) yet. I have not heard of anyone having any sort of problem with them yet. I also came from a 22re that I had done the timing job on just in time and am very paranoid about it.