SP2010 Custom master with People Picker and Lookup columns

I am creating a new post since the original was marked as answered however it was never answered. 

When using a custom master page, people pickers throw an error (unexpected) and lookup column dropdown boxes do not expand.  Modifying the custom master for the people picker might resolve the bug for that particular control (only if it is permitted and in production environments this is not feasible) i need to get another resolution to these issues.  Can someone give a parameter that can be placed in a content editor web part that will set the IE version to IE8 or is it possible to get upgraded controls that work with IE9. 

On a larger scale, does this mean that custom master pages cannot be used in SP2010?  I have a custom master on a project that my team has been working on for 5 months.  I was planning to go live with it in January.  Do I need to go back to the user community to let them know that it has to be redeveloped in .Net from scratch and will not provide any SharePoint capabilities (search, versioning, workflows...)?