Pattern p = Pattern.compile("\\b(?:Input|Calc)![A-Z]\\d+\\b");
(?:Input|Calc) — either keyword
! — the literal exclamation that both forms share
[A-Z] — exactly one uppercase column letter
\\d+ — one or more digits
\\b — word boundaries so you don’t bleed into adjacent text
Quick test with your samples
Matches found:
ADD(Input!A34 + Calc!D93) → Input!A34, Calc!D93
Input!D343 = 1000 → Input!D343
Calc!D71=IF(HasValue(Input!D4), "…") → Calc!D71, Input!D4