If anyone's interested, I'll post the significant additional scenes that appear in the novelization. Many of these were likely included in the original cut of the film. (Certain parts may have been included in the final cut as well, and I've simply gotten the different versions mixed up: novelization, comic, film.
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Here's part one:
Orellana's Death
A brief prologue where we see Orellana trying to return the skull, and being driven mad in the process. He makes it to the Chauchilla Cemetery and the "living dead" overtake him.
Yucatan Pennisula 1957
Indy is crawling beneath a Mayan city, while Mac is outside warning him that a tropical storm is fast approaching. Indy crawls toward the statue of a serpent, and ultimately falls down its mouth into an underground river. He's washed out through the side of a cliff, and uses his bullwhip to swing to safety. Meanwhile, the Russians invade Indy's campsite. When Indy finally returns, he finds everyone dead except Mac. The two are taken prisoner.
Spalko Operates
This occurs after Indy has survived the A bomb, and Spalko has returned to her base. As three top Russian officials look on, Spalko dissects the Roswell alien in a small operating room. As the officials leave, they coldly inform her that she is not to fail.
The Dean's Speech
At Indy's house, the Dean offers Indy another piece of advice. He points out that the youth are always asking,
"Who will I be?", then later proclaiming,
"This is who I am!". But at his age, he has begun to ask,
"Who will they say I was?" This affects Indy and leads him to think about his legacy.
The Football Stadium
Just as a crucial play is about to begin, the motorcycle pursuit bursts onto the field. The quarterback, realizing the other team has backed off, launches a perfect pass. Indy ends up catching it and the crowd applauds. He then throws a pass of his own- through the car's open window and into the head of the driver. (This scene would've appeared in between the student protest and Brody's statue.)
Fortune and Glory
Prior to leaving his house with Mutt, Indy pauses to examine a sketching of Akator. He remarks to himself:
"Akator. Where Oxley was taking the skull. If it exists, it would be the find of a lifetime. Make a reputation even politicians can't touch." Presumably, this would've explained how he intended to avoid further pressure from the government.