They are all grammatically correct. No preposition would produce a grammatically incorrect sentence. However, with some prepositions it might be quite difficult to figure out a meaning. Perhaps with some difficulty I can imagine a context for every single one of your six sentences that makes sense. However, I have the most trouble imagining such a context for "in". Since that is the hardest one for me to defend, I accept the challenge: "Tom planned to spend the evening studying English. His plan was to spend 15 minutes on verbs, 15 minutes on words (vocabulary), and 15 minutes on grammar. First he did the verbs. Then he did the grammar. But then he ran into unexpected difficulty with the third piece. He was stumped in words (meaning he was stumped in that category). He had never before seen so many words containing the letter 'z'!"

Stumped for words is a fixed expression and the only one them that is used.

#1 is correct. It means that Tom wanted to express an idea, but couldn't find the right words to do it. It is the only natural sentence in the list. #3 is correct, but it is unnatural to say and it has a different meaning. It seems to mean that there were many words that Tom couldn't understand, or that Tom doesn't related to language well. "Tom was a simple person. He understood actions, but he was stumped by words." The others are weird and unnatural. I don't think the problem is "grammatical." I think it is just more of a question of usage and colocations. Some words just pair with some prepositions and not others. These sentences could all be correct with words other than "stumped." 2: "Tom was very voluble. He was overflowing with words." 4: "Tom was a verbal person; he swam in words." 5: "Tom grew up a literate household. You could say he was raised on words." 6: "Tom's job was writing, but he never took it seriously. He liked to play at words."

I would say stumped for words is the generally accepted phrase. Most English phrases are not able to stand on their own, so context matters.