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For example if the term 'company' is used through out a page and the word 'business' is used 3x more in searches. Would it be wise to change that change and do similar changes throughout my websites for all words?
Is that a standard SEO practice? And finally are there any programs that assist in doing this?
If you feel you could be competitive in the area that is searched for three times more, go for it. But if this different area has 3 times as much competition and/or the competition has better SEOers then you may see less results from changing the word.
For example (this is a made up example):
The term "widget company" is searched for 1,000 times in a month on google and it has 100,000 google results.
While the term "widget business" is searched for 3,000 times in a month on google but it has 1,000,000 results.
If you are listed in the top ten now for "widget company" you could be getting maybe 100 clicks per moonth. If you changed your words to "widget business" there is a chance you will no longer be listed in the top ten. Not being listed in the top ten will kill your click amounts and you will probably see less returns.
I'd say change it and see how it works out a few weeks later. If you aren't seeing higher returns, change it back.
Of course, I don't know the details of your site so I am just making a broad generalization.