You are right.. you will not get CRM context inside that WebApp as both are running in different application pools. Now if you want to have that kind of functionality you will two ways I can think off. 1. Recreate a new custom popup form with similar CRM functionality. This will involve development and you may not get same look and feel as well. 2. Create a new Web Resource with the desired functionality which you are planning to have in webApp. This will give you better control and will be shipped with CRM to other environments as well. Apparently this will be hard work as you will have to play with HTML and JS a lot in absence of a designer support. Hope this helps,
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