When getting rid of GO TOs through a systematic series of transformations, begin by eliminating the use of sections in the PROCEDURE DIVISION.
(In some cases, as in the use of declaratives, you cannot avoid the use of sections. In that case your best hope is to rewrite each section separately as needed.)
Make sure that each EXIT paragraph has a unique name within the entire PROCEDURE DIVISION (not just within the section). If a section already has an EXIT paragraph, you may need to rename it.
The new EXIT paragraphs are safe because they do not affect any existing flow of control. When not the target of an active THRU clause, the EXIT paragraph behaves like a CONTINUE statement.
PERFORM A.
PERFORM B.
PERFORM C.
In the presence of GO TO, however, this transformation may not be safe.
Suppose A contains GO TO C, thereby bypassing B.
Another possible problem is a PERFORM THRU where the target of the THRU clause is somewhere in the middle of a section. Perhaps you can rearrange the paragraphs and direct the THRU clause to the EXIT paragraph. However, you must be aware of the possibility that the section will receive control, not only through a PERFORM, but also by a GO TO, or by a fall-through from the preceding section. In that case the flow of control is different.
Such contortions may be difficult to unravel. Proceed with caution.
One way or another, your goal at this point is to ensure that:
When you PERFORM a section without using a THRU clause, control returns to the PERFORMing code when it reaches the next SECTION header.
With a PERFORM THRU, control returns when it has executed the target of the THRU clause. Since you have put that target at the end of the section, the results are the same as if there were no THRU clause.
You may need to rename some paragraphs so that the names will be unique within the entire PROCEDURE DIVISION, not just within a section.
Consequently, you should not follow these guidelines blindly. Be aware of the more perverse possibilities, if only so that you can rule them out. If you find a particularly twisted bit of logic, you'll just have to wrestle with it by any means necessary until it takes a more familiar form.