I'm in the exact same situation as http://social.technet.microsoft.com/Forums/forefront/en-US/a5b74a42-574d-4588-80ad-fd4ad82b0ee5/the-request-failed-because-url-is-too-long The workaround provided by Ben didn't work for me.
UAG Version: SP3 RU1
Here's a sample URL which is too long:
ADFS: resourcests.customer.be
Trunk: public.customer.be
Published app (non-claims): appportal.customer.be (just static site with no authN on it)
Any thoughts?