Let it get kind of firm, still tacky but won't string when you touch it. 15 minutes to a half hour, depending on the RTV and the temp.
I used a real thin layer of the rtv and its been working just fine on my car. I also used the end pieces I wouldnt suggest throwing them out. all you need is a real lite layer of sealer to help everything stay put
NOOOOOOO!!!!!!!!!!!!!!!!!!!! That stuff is THE worst thing to use when it comes to engine assembly. Do as Bryant suggested, and go thru the torque sequence at least 5 times, then let it sit a few minutes, then go thru it again. I use Permatex Ultra Blue for assembly, with a thin film around the coolant ports and a dab in the corners where the gaskets meet. I ALWAYS use the end gaskets. The corks now have an adhesive on the block side to keep em from squeezin out. I use the rubber seals if the block has the locating holes for them. If you have not removed the intake yet, try retorquing it again before pulling it to see if the leak stops.
I would recommend "The Right Stuff", comes in a can with a nozzle like Ready Whip and black in color when it comes out. It's the only thing that would stop my thermostat housing from leaking. I also used it on the 3rd member housing without any gasket and has never leaked. Bit expensive but worth every cent!!