How do I stop iTunes 11 from randomly match SD and HD episodes of a TV-series?

I'm trying to add my entire TV-series collection to iTunes so I can easily view it on my AppleTV. Everything was great until I tried to add DVD-rips and BD-rips of the same show. Now it just randomly matches the qualities. It might match Season 2 episode 4 (DVD) with Season 4 Episode 9 (BD). Some series from Blu-rays are in 720p and some in 1080p, and I have the same problem with them! iTunes matches them completely at random. I've been trying everything (or at least what it feels like)!

Tags I've used are different between episodes: Episode name, Release date, Sort episode name, Short description, Long description, ContentID, TV Episode number, Track number.

Tags shared within a season: Copyright, XID, TV season number, Album, Disk number.

My temporary (and very, VERY space consuming) solution has been to make each and every episode in all the lower quality ratings available – a 1080p episode will be made into both a 720p and SD file also, a 720p will also be made into an SD file. I have over 4,000 episodes in my library, and it's very annoying to have at least two qualities of all of them.

Anyone out there that has a solution? How do I make iTunes understand that Season 3 Episode 10 and Season 6 Episode 5 are different from Season 1 Episode 6?

Have you tried directly editing the info in iTunes? For example, you can manually select all of the season 4 TV shows, right click, press the "Get Info" button (Not what most people expect)

You should see a window like this (when selecting multiple items), which you should be able to directly modify the season number: