Your keys and pfx should never live on the file system. One slip up could serve your files to the internet and now everyone can get your key. Storing them in the windows cert store is best.
Yes. You should do all the ssl configuration on IIS and Windows.
This is what I have used on production.
On the application, you should simply write:
var app = express();
app.listen(process.env.port);
Then web.config for iisnode should look like this:
<configuration>
<system.webServer>
<handlers>
<add name="iisnode" path="app.js" verb="*" modules="iisnode" />
</handlers>
<rewrite>
<rules>
<rule name="HTTP to Prod HTTPS redirect" stopProcessing="true">
<match url="(.*)" />
<conditions>
<add input="{HTTPS}" pattern="off" ignoreCase="true" />
</conditions>
<action type="Redirect" redirectType="Found" url="https://{HTTP_HOST}/{R:1}" />
</rule>
<!-- Don't interfere with requests for logs -->
<rule name="LogFile" patternSyntax="ECMAScript" stopProcessing="true">
<match url="^[a-zA-Z0-9_\-]+\.js\.logs\/\d+\.txt$" />
</rule>
<!-- Don't interfere with requests for node-inspector debugging -->
<rule name="NodeInspector" patternSyntax="ECMAScript" stopProcessing="true">
<match url="^app.js\/debug[\/]?" />
</rule>
<!-- First we consider whether the incoming URL matches a physical file in the /public folder -->
<rule name="StaticContent">
<action type="Rewrite" url="public{REQUEST_URI}" />
</rule>
<!-- All other URLs are mapped to the Node.js application entry point -->
<rule name="DynamicContent">
<conditions>
<add input="{REQUEST_FILENAME}" matchType="IsFile" negate="True" />
</conditions>
<action type="Rewrite" url="app.js" />
</rule>
</rules>
</rewrite>
</system.webServer>
</configuration>