we are considering for our first trip to japan going to tokyo for 4-5 days then going to hakone overnight then from hakone going to kyoto for 2-3 days before we have to go back to tokyo to depart.

is this reasonable? or should we skip one section of our trip?? (ie just do tokyo and kyoto or just do tokyo and hakone?)

can we leave kyoto in the morning and still get to the airport in tokyo in time for an evening departure??

can we use the JR east rail pass for this trip?

I think this is feasible, but I would think about more time in Kyoto and less in Tokyo. Think about taking 1 or 2 of your Tokyo days and adding them to Kyoto instead.

during out time in tokyo we were planning on doing two day trips (one to nikko and one to kamakura) so we only end up spending 2-3 days in the city tokyo total-

here is what we are considering

arriving in tokyo sept 2 late afternoon

depart tokyo for hakone sept 6 for one night

depart hakone sept 7- go to kyoto till the 11th

depart kyoto on the 11th for tokyo- leave later afternoon for the US

Yes, it's reasonable.
Yes, you can make it from Kyoto to Narita in time for your flight, probably.
No, you cannot use the JR East Pass for Kyoto.

Time for you to go and buy the Fodor's book on Japan, or contact the JNTO, or get a travel agent.