Andria,
You're making it way to hard by doing things in the wrong order.
The ideal way is:
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get your site working with your current version of mojoPortal
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upgrade to the latest 3.5 .NET version of mojoPortal
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visit the /Setup/Default.aspx page
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now upgrade the latest .NET 4 version of mojoPortal you will get an error
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change your control panel settings to use .NET 4 to fix the error
another way it can work:
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get your site working with your current version of mojoPortal
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upload files for the latest version .NET 4 version of mojoPortal
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now you get an error so now you need to change the hosting control panel settings to 4.0 .NET
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next visit the /Setup/Default.aspx page
If you use the 3.5 .NET version of mojoPortal under .NET 4 you will get an error so you need to change to 3.5 aka 2.0 .NET in your control panel.
If you use the 4.0 .NET version of mojoPortal under .NET 2.0/3.5 you will get an error so you need to change to .NET 4 in your control panel.
You're just going back and forth on the above two configuration errors.
Hope it helps,
Joe