I dont know what a adoption decree is.. but the koseki shohon shows the adoptions...
In most countries the adoption process is dine by civil courts. An adoption decree is a court order approving the adoption.
According to the State Department info, in Japan adoptions are done through a family court system:
http://adoption.state.gov/country_information/country_specific_info.php?country-select=japan
I am pretty sure that koseki will not be sufficient and that they'll request you to provide a copy and a translation of the original adoption decree.
Japan is not a party to the Hague Convention regarding international adoptions, and the officers adjudicating your passport application will need to make sure that your adoption does conform with the requirements of the U.S. nationality law for derivative citizenship. In particular, my understanding is that they'd need to verify that at the time of adoption the other biological parent (in this case your biological father) was either deceased or that all the parental and custodial rights of that biological parent had been terminated. Things like that are usually spelled out in the adoption decree or some other supporting paperwork.
Also, as noted above, for CCA eligibility you'll need to provide proof that you resided with your step-dad in the U.S. at some point betweeb Feb 27, 2001 and your 18th birthday. You'll need to provide school records or some other proof to demonstrate this.
Also (although I am not sure about this), I think you'd need to provide proof that after the adoption you have resided with your step-dad for at least two years, and you may have to provide school records or other proof for a more extended period because of this.
You really should have collected more documentation and should have talked to an immigration lawyer before submitting a passport application.
At the end you may find that completing your pending N-400 process may be easier that completing your current passport application.
As Jackolantern wrote in his earlier posts, regardless of your pending passport application, you should still go ahead and request a Status Information Letter from the SSS and sent it to the IO adjudicating your N-400 together with the N-14 form you have gotten (if you have not received the status information letter by the Oct 6 deadline, request an extension of that deadline. Even with the status information letter your N-400 might still be denied on GMC grounds, but you should not abandon the N-400 process yet, given the complexities of your CCA-based passport application.
In your place I'd also still consult an immigration lawyer now regarding your pending passport application.