Your extra long renders are caused by the extruded text. If you must use extruded text put just the text in a Ray-traced comp and nest that in a Classic Comp. Make sure to trim the extruded text comp so that it is only as long as it must be. Make sure that your GPU drivers are up to date and that AE is using the GPU to render the ray traced comp.
The AME is the way to go for all h.264 renders. The you-tube presets are very good and easy to use. Rendering h.264 movies from the Render Cue never has been a good idea and in the CC version, this option was deprecated (removed but available again through the preferences) because it is not good for much of anything and cannot produce professional results.
Also, make sure that you didn't starve your other apps for memory in the memory settings. I'm assuming 8GB ram, make sure that at least 3 are assigned to other applications. Timewarp can be a render hog and it may be faster in the long run to pre-render that layer to a production codec and replace the layer with the render. A temporal effect stacked up with a bunch of other layers and effects can really slow things down.
If you make a list of all the differences between a comp that takes an hour or two to render and one that takes 15 we can probably figure out where the bottleneck is and help you solve the problem.