Why shouldn't the Senate be connected to the states? The House of Representatives is. Unless you are planning on getting rid of states completely (and all of the state-level laws, regulations, taxes, public representation, correctional facilities, etc.), you have to ensure Congress consists state representatives. Our entire country is built on the concept of different levels of government with different levels of authority. By removing state representation, you are essentially talking about a fundamental recreation of our government.
You say that it is insane that New York gets the same number of senators as North Dakota. Why is that insane? We have the House of Representatives to ensure that people are represented in terms of population. We have the senate to ensure the needs of the less populated states are not simply ignored. Because the Senate and House represent the population in different ways, different needs can be addressed, which forces compromise. The conflict between the Senate and House also will delay bills and limit heat-of-the-moment and knee-jerk bills from being passed to quickly... this does not always happen, but it does to an extent.
You want an automated system to create districts that ignore states. Well, even if you ignore the concept that our entire federal legislative system is built on the idea of state representation and such a change would mean a recreation of our country's government, how would you create such a system that was fair to all? It would obviously have to be dynamic to change as the population changes. But a change in the algorithm to create the states could have just as much of an affect as intentional gerrymandering. In many cases, large cities have very different needs than the rest of the state. If an automated system made a put a large city in a single district, then you have 1 district that will view things a certain way. If the automated system split the city into quadrants and included a little bit of area around the city, then you will have 4 districts that represent the city that will also override the needs of the areas surrounding the city. What type of automated algorithm can be created that is fair to all? Gerrymandering is typically done by parties. An automated system could potentially be far worse, IMO