I am seeing a CUP verification error in the log since it appears that the server is not signing the responses using CUP.
I am pasting a couple of relevant log lines. Please see the highlighted log lines.
My advice would be to hack a local build to that ignores CUP verification then make the changes needed to have a functional end-to-end updater for your product. After everything is sorted out, then you could focus on CUP part.
Please be careful with customization of Omaha so that the custom installer does not conflict with Google's Omaha.
[11/06/16 12:55:44.528][GoogleUpdate:goopdate][3428:4180][sending web services request as UTF-8][<?xml version="1.0" encoding="UTF-8"?><request protocol="3.0" version="1.3.99.0" shell_version="1.3.99.0" ismachine="1" sessionid="{509110D9-9719-441F-A2A0-9E9BACC4FFFB}" installsource="otherinstallcmd" testsource="auto" requestid="{69331E50-DC57-46BC-B2C4-BAFF783457C2}" dedup="cr"><hw physmemory="4" sse="1" sse2="1" sse3="1" ssse3="1" sse41="1" sse42="1" avx="1"/><os platform="win" version="6.3" sp="" arch="x64"/><app appid="{9B01C5D1-7F78-4A4E-A89B-0415F6466BC7}" version="" nextversion="" lang="en" brand="" client="" installage="-1" installdate="-1"><updatecheck/></app></request>]
[11/06/16 12:55:44.544][GoogleUpdate:goopdate][3428:4180][Send][url=http://192.168.2.2:9090/service/update2][request=<?xml version="1.0" encoding="UTF-8"?><request protocol="3.0" version="1.3.99.0" shell_version="1.3.99.0" ismachine="1" sessionid="{509110D9-9719-441F-A2A0-9E9BACC4FFFB}" installsource="otherinstallcmd" testsource="auto" requestid="{69331E50-DC57-46BC-B2C4-BAFF783457C2}" dedup="cr"><hw physmemory="4" sse="1" sse2="1" sse3="1" ssse3="1" sse41="1" sse42="1" avx="1"/><os platform="win" version="6.3" sp="" arch="x64"/><app appid="{9B01C5D1-7F78-4A4E-A89B-0415F6466BC7}" version="" nextversion="" lang="en" brand="" client="" installage="-1" installdate="-1"><updatecheck/></app></request>][filename=] [11/06/16 12:55:44.544][GoogleUpdate:goopdate][3428:4180][Trying config: priority=2, source=auto, wpad=1, script=]
[11/06/16 12:55:44.544][GoogleUpdate:goopdate][3428:4180][trying CUP-ECDSA:winhttp]
HTTP/1.0 200 OK
Date: Sun, 06 Nov 2016 07:10:47 GMT
Content-Type: text/xml; charset=utf-8
Server: WSGIServer/0.1 Python/2.7.12
Vary: Cookie
X-Frame-Options: SAMEORIGIN
[11/06/16 12:55:47.644][GoogleUpdate:goopdate][3428:4180][WinHttp status callback][003E3F78][handle=003CC650][data available]
[11/06/16 12:55:47.644][GoogleUpdate:goopdate][3428:4180][WinHttp status callback][003E3F78][handle=003CC650][receiving]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][WinHttp status callback][003E3F78][handle=003CC650][received]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][WinHttp status callback][003E3F78][handle=003CC650][connection closing]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][WinHttp status callback][003E3F78][handle=003CC650][connection closed]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][WinHttp status callback][003E3F78][handle=003CC650][read complete]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][WinHttp status callback][003E3F78][handle=003CC650][data available]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][WinHttp status callback][003E3F78][handle=003CC650][read complete]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][bytes downloaded 722]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][SimpleRequest::Send][0x0][200]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][CUP-ECDSA][etag: ]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][CUP-ECDSA][ETag empty, rejecting]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][HttpRequestInterface::Send returned 0x80040880]
[11/06/16 12:55:47.659][GoogleUpdate:goopdate][3428:4180][Send request returned 0x80040880. Http status code 200]
[11/06/16 12:55:47.737][GoogleUpdate:goopdate][3428:4180][Send response received][result 0x80040880][status code 200][<?xml version='1.0' encoding='UTF-8'?>
<response protocol="3.0" server="prod">
<daystart elapsed_seconds="25847" elapsed_days="3597"/>
<app status="ok" appid="{9B01C5D1-7F78-4A4E-A89B-0415F6466BC7}">
<updatecheck status="ok">
<urls>
</urls>
<manifest version="0.0.1.0">
<packages>
<package required="true" hash="BLBiqD2yQ+Ubp9sAAOvkJ7fhpjg=" name="installer.exe" size="1228800"/>
</packages>
<actions>
<action successsaction="default" run="installer.exe" event="install"/>
</actions>
</manifest>
</updatecheck>
</app>
</response>
]