Find the tell application as follows

tell application “Yojimbo”
set db_id to make new note item with properties {contents:_contents, name:_name}
add tags “inbox” to db_id

Then to create a mail act-on rule that runs the script as:

~/Library/Scriptis/MailToYojimboinbox

And your mail message will be added to yojimbo with the tag of inbox so you can find it later and add extra attributes; and then clear the inbox tag.

-or- if you prefer you can create a script the send to yojimbo and then activates yojimbo so you can finish the processing example:

tell application “Yojimbo”
set db_id to make new note item with properties {contents:_contents, name:_name}
add tags “inbox” to db_id

activate
– hack to “show db_id” by opening it as a URL
open location “x-yojimbo-item://” & (id of db_id)