I am playing with the Twilight Imperium 3rd Edition Core Game, the Shattered Empire Expansion, and the SHards of the Throne Expansion. Over time, I have taken out cards as need be, such as if they apply to a game mechanic I no longer use, however I have multiple printings of certain cards, cards that refer to options I don't use, but are NOT optional use as trade goods. What should the proper contents of my deck be? I feel as if 174 cards is a bit too much…

I don't know offhand, but if I had to reconstruct the Action Card deck from a random pile of Action Cards, I'd do the following:

• Sort all the Action Cards into three piles: (1) base game, (2) Shattered Empire, (3) Shards of the Throne.
• Start with the pile from the base name.
• Read the Shattered Empire ruilebook on which cards to remove from the base game cards, replace with cards from Shattered Empire, and which cards from Shattered Empire to just add right in.
• Read the Shards of the Throne ruilebook on which cards to remove from the base game cards, replace with cards from Shards of the Throne , and which cards from Shards of the Throne to just add right in.

I'd think that'd give you the entire set as it "should be" according to the rules.

After that if there are Action Cards you prefer not to use, just remove them from the deck.

I don't think I understand the question. All the cards from each expansion are marked with the symbol of the expansion they came from, so if you want to rebuild the core deck all you need to do is sort the cards by their symbol (or lack thereof, for the core game.)

If you're asking us which cards should be left out based on your house rules… I don't see how anyone here can help you with that. They're your house rules, and which cards are considered useless due to rules you've left out is a decision only you can make.

Also: The Action Card deck IS supposed to be so big that it's highly improbable that you'll ever go through it in any game. This is to promote variety.