After finding myself in several similar situations where I needed to get a job done quickly with BizTalk but it just wasn't playing ball, I decided to do something about it. I developed a send adapter for BizTalk that integrates with Windows scripts.
Because scripting is so easy and fast, I find that for certain tasks, productivity can go through the roof using the Script Adapter. Simply develop a script (say using VBScript) and implement a procedure called OnMessage where all your code goes. Then, when BizTalk receives a message and forwards it on to the Script Adapter it will load your script and call your OnMessage procedure. Simple as that.
For a two way send, just return a string value from the procedure. The Script Adapter converts the string in to a message and returns it BizTalk.
Be warned, this is a first release. Consider it a beta. So I would appreciate feedback on it.
You can get the Script Adapter at my employer's website, Thinkscape: Download the BizTalk Script Adapter.
[Update 2007-07-30 - Note that the Script Adapter was previously hosted at Got Dot Net but Microsoft has closed the site down. Thinkscape have been kind enough to host the adapter, and even better, they will be providing support and working on enhancements - and it's still free!]
Note that on installation of the Script Adapter there is a choice to install it for Everyone or Just Me. Sometimes I have found that selecting Just Me can cause issues when you come to register the adapter with BizTalk (something to do with registry access permissions I think). Therefore to be on the safe side install it for Everyone
There is a guide included with the installation that walks you through setting up the samples. That should hopefully clue you up enough to develop your own scripts for the Script Adapter.