My unit outside is a Payne 4 ton (Model PA 13NR 048-H) and inside is a 3 1/2 ton. Recently my blower motor was replaced on the unit inside and the repairman told me the units should be the same size and should not be running. The have been in place for over 7 years. Should I be looking at something besides the tonnage?

You tell us. Except for the current problem has it been working OK? Ideally the units should be exactly matched, but a mis match as your may work just fine. Is that the case?

A 1/2 ton difference is not that much in the overall scheme, 42,000 BTU vs 48, 000 BTU. As long as they are both the same Freon, most likely R22 based on "over 7 yrs", If it hasn't caused a problem as of yet, keep it .

You tell us. Except for the current problem has it been working OK? Ideally the units should be exactly matched, but a mis match as your may work just fine. Is that the case?

Except for the fact that the outside unit is 7 years old and the inside unit is 24 years old, this is the only issue we are having now. We have had the issue of rust in the drainpan, but our pan is metal, so is to be expected. We have not had issues with that for at least the last 4 years.

A 1/2 ton difference is not that much in the overall scheme, 42,000 BTU vs 48, 000 BTU. As long as they are both the same Freon, most likely R22 based on "over 7 yrs", If it hasn't caused a problem as of yet, keep it .

I was told by my warranty company that the outside unit cannot be 4 T and the inside unit 3 1/2 (it could be visa versa). Is this true?

"Warranty" companies are basically insurance companies... they will tell you what they need to to keep from paying for claims