... replace the first entry in file1.txt(JO EMS Math) with my row in file2.txt (Jon EMS Physics) without changing the row format like padding and spacing.

I don't understand what "padding" means in the context of your question. (In general, I don't understand the context of your question.) I don't understand how "spacing" can be expected to remain the same when two of the three replacement fields have different widths.

I stored and worked on @ ...

I don't understand what @ is.

... and was able to do the replacement however the padding and spacing changed.

Can you please show a Short, Self-Contained, Correct Example of what you have done so far? It might do much to clear up my misunderstandings.

Also: Is this a school assignment? It sure looks like one. If it is, please tell us and we will be better able to offer appropriate help.

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