The Lovecraft story did differ a bit. This is from memory, haven't read it in a while.
First off the single mom in the movie doesn't exist in the book, the main character is just given a baby whom he has no prior relationship with.
No computers in the story
Masurewicz still is the crazy old coot but in the story Gillman only makes mention of meeting Masurewicz.
The ending is very much like the story, spare that there is a brief paragraph or two where a group of workers are tearing the house apart and discover the body of a rat...but with a skull with human features.
Thats all I can recall right now. Gordon does do a very good adaptation with the story and I definatly can say this is far closer than Re-Animator was.