You remember one point wrong, it was not the scientist who got swallowed by the giant amoeba creature and spit out as a skeleton but his treacherous friend, he pretends to be his friend but has lecherous intentions on the scientist-hero's girlfriend.
The villain gets contaminated by this creature and his inner corruption comes to the surface and he tries to kill the hero.
The monster in this movie is an ancient creature that dwells deep in the earth and was responsible for wiping out the Mayan civilization overnight.
Now that I think of it, Dean R. Koontz's PHANTOMS is clearly based on this movie.
If you've not read that 1983(not the 1998 film) book of his, then do so now.
It is in my opinion his best work.
I thought that was the one. The trailer creature came really close to what I remembered.
I also did read Phantoms, and saw the movie.
Picked up Caltiki earlier on Ebay for nine bucks, BTW.