Viserys dies next week (Episode 6). This is also when Bronn saves Tyrion and they get dumped in the Vale. Tyrion negotiating an alliance with Shagga happens either in 6 or 7.

Eddard discovers 'the truth' in Episode 7, WIN OR DIE. He has his confrontation with Cersei in the garden and tells her he knows and advises her to flee. This is when Cersei says, "In the game of thrones, you win or die."

Eddard's arrest might happen at the end of Episode 7, but definitely no later than Episode 8, THE POINTY END. The episode is called this as it's the first time Arya has to use the pointy end, i.e. on the stableboy as she flees the Red Keep during the coup. Episode 8 also marks the point where Tyrion joins up with his father's army and meets Shae.

Robb Stark's army reaches the Twins and Catelyn treats with Lord Frey in Episode 9, BAELOR. Episode 9's cliffhanger ending is Eddard's execution. In the book he is beheaded on the steps of the Great Sept of Baelor, hence the name. From the timing that means that the Battle of the Green Fork is also likely in Episode 9.

You are right that this leaves a lot to do in 10, including the Battle of the Whispering Wood and Jaime being taken prisoner before word of Ned's death reaches Robb. However, they are ending the season before the liberation of Riverrun. Riverrun, as a location, and Edmure and Hoster Tully's introduction has been put back to Season 2. However, as it's such a great ending, I suspect the 'King of the North' scene will still happen in 10, just with the riverlords and northern lords present.