Eric,
It was 18 holes packed very tightly from the looks of old aerials. And you're correct, it appears that the large ponds were dug to provide fill and elevation because the old course looks like it had no interior ponds.
Yes, the only water before was the lagoon on the east side. It wasn't in play. The addition of the ponds and fill has really helped with drainage.
I lived a few blocks away from the old clubhouse from '90-'93. I had a monthly pass for most of that time so I played many rounds there. There was no architectural interest in the old course except for the unsual opportunity to hit directly over large oaks that were blocking the tee shots on two of the par fours. The interior holes had such little interest that I cannot picture them now despite playing them many many times.
Stan Stopa the pro was mentioned in the OP. I remember him as a nice guy and very good player. He had a plaque or a sign behind the desk of the shop commemorating his All America honors. I believe he was in the same class that included Lanny Wadkins and Tom Kite. He qualified for the Freeport-Mcmoran at English Turn one year when I was there.