I don't believe so.

You can "get an idea" if it came from a 4spd car because the crankshaft will be drilled in the back. Automatic crankshafts "normally" aren't drilled for the transmission pilot bushing, but no guarantee of that.

How SURE are you that the engine came out of a 69 Roadrunner?

I've seen some "numbers gurus" that can tell things from block numbers like:
a) must have been made in Plant X on the 2nd shift
b) Plant X only made certain cars & not others

What I'm getting at is that IF the engine came out of a C-body, & "most" C-bodies didn't come with 4spd, then the engine "probably" has an automatic (not drilled) crank. If it's for sure out of a Roadrunner, then "maybe" or "maybe not" the crankshaft is drilled for a 4spd.

That's all I've got....sorry not more.