I have a 2009 4 door JK with 53000 miles. 3.5 inch lift, 35" tires, snorkel, heat extracting hood, in South Texas. About a month ago I started to notice a power loss when shifting from 3rd into 4th, now I'm getting intermittent 3rd gear power loss. I seems to correct itself about 20 minutes after driving around. Any ideas what could be causing it? (its South Texas, so not real cold down here).

 

It looks like you have a manual transmission (info in your profile). When you lose power, are the RPMs rising? Is it just a momentary loss of power and then things kick in? Most obvious thing would be that the clutch is slipping. 53k miles sure isn't much, but we are talking 10+ years old now.

 

RPM's don't rise, usually for up to ~20 mins. Then something changes, and then I can use 3/4th gear. (and correct on Manual)

 

Have you checked for codes. I have an Innova 3100 scanner and it is simple to use and very useful. It was $109 on sale here.