[MOSS/WSSv3] Change the application pool of a web application

[ISSUE]
How should I change the application pool of a web application

[BACKGROUND]
Recently I ran into a situation where Microsoft had performed a MOSS Risk Assessment Program (MOSSRAP). One of the recommendations of Microsoft was to limit the amount of application pools used on one environment. Depending on your hardware specs, this number will be around eight. However the administrators had created about 50 web applications and configured an application pool for each one of them.

In order to adopt the Microsoft recommendation, the administrator went into IIS and changed the application pools manually. When they tried to add a new server to the farm, this triggered a reset of the configuration on all servers, basically resetting the application pools to the configuration known by SharePoint (each of the web application in its own application pool. This brought down the entire environment for several hours.

[TECHNICAL DETAILS]
During installation/configuration of SharePoint, SharePoint stores all configuration on web applications and application pools. It does that so it is able to deploy everything to a server which is joined to the farm with the correct settings. When you make manual changes to IIS, the settings in IIS do not match the configuration known to SharePoint and you might end up in deep shit.

[SOLUTION]
Unfortunately it is not possible to change the web application/application pool configuration via Central Admin. The only way is by using the SharePoint object model. On the Internet I found an article which described how you could use a PowerShell script to accomplish this configuration change:
Change application pools via PowerShell

This script did have one downside: It changed the configuration in SharePoint, however it did not change the configuration in IIS. To solve this, I found a method added to the SPWebApplication class in one of the Cumulative Updates called ProvisionGlobally. By using this method, you provision that specific web application on all servers running the web front end role. You can download the revised PowerShell script here.

After running this script the old application pools are still present in SharePoint AND IIS. In order to delete them from IIS, you need to write a script to Unprovision them. However the SPApplicationPool class does not have an UnprovisionGlobally method, so you need to run this script on each of the WFE servers.