This sounds like something mouser's Clipboard Help+Spell is designed to do, though. But I don't think it (currently) has this feature
Not running CHS on this computer, so can't check - but CHS allows you to add your own filters, so you could use something like a SED script or one of the command-line search and replace tools. This won't be completely seamless, as the OP seems to want. You'd have to pop up CHS's main window and choose the filter, but, that method allows you as many search and replace pairs as you want.
If you want seamless, take a look at Clippy
- you need the beta - one of its operations is given as
Name: Search and replace
Description: Replaces all occurrences of a string with another string.
Number in ini file: 28
Parameters: search string, replace string
Don't know if that's only one string or whether you can define multiple strings.
Boxer Software's TextMonkey
is in similar vein, but more powerful; it comes in both payware and cut-down freeware versions. Search and replace is a built-in function. It allows up to four search-and-replace pairs.