"For a time she had seemed to read his mind translating what ..." - You need a comma after "mind" to show that it is Laura who is translating, and not his own mind (does that make sense?).
"When he had tried to speak it had come out wrong ..." - To make this sentence more active, take out the "had"s and change it to "came out wrong".
"Lavender" - This doesn't need to be capitalised.
" ...and removed it from the flower bed putting it in his pocket." - You need a comma after "bed" to show that it is Danny putting the weed in his pocket, not the flower bed. I know it is obvious, but grammatically, you need to show this.
"Danny thought to himself, yes that makes sense, that is how the word should be said. and he nodded." - The period here should be a comma.
"She's not remarried you know and is in a bad way." - I would put commas either side of "you know"
"The buttons were bigger here than on the old laptop or the phone and he could type" - You need a comma before "and."
"Are you two back together, Oh praise God!" - It should be a period instead of a comma after "together." Also, I would place a comma after "Oh." Or, even, an exclamation mark would work.
"Sounds like a plan and will you?" - You need a comma after "plan."
"Already done it Pastor and ..." - You need commas either side of "Pastor" because Danny is addressing him directly.

"What are you fighting about." - You need a question mark at the end of this sentence.
"On the third ring, several seconds after that is when James sits up in his chair literally." - Firstly, you need a comma after "that" to make the sentence clearer. Also, delete the word "literally." It is not needed here.
"James goes leave the living room" - I would delete the word "leave" as it doesn't make sense. "Into" would make more sense.
When Patrick visits James, I got really confused. You write, "'Matt, Claire, James. Is anyone there?' Patrick asks. 'I need to talk to you. It’s about your little sister Alice.'” - This is the first mention of Alice, and as Patrick was speaking out to all three people, I didn't know whose sister she was.

"Mr. Zhou appeared from between two aisles near the back door, 'You be careful ...'" - It should be a period instead of a comma.
"He pointed up, and said, 'I do not go far, just upstairs ...'" - There shouldn't be a comma after "up."
"He’d mentioned more than once his move to Novica had been partially based on the low crime rates. 'I’ll be back in a couple of days ...'" - I would move the speech down to a new paragraph because when I read this, at first, I thought "He" was speaking, but it wasn't him, it was Sam.
"' ...the book you ordered will be here the day after tomorrow,' he informed me." - You don't need this dialogue tag. It slows the action and is unnecessary because we know already who is speaking.
"I searched the shadows for any sign of movement, and saw nothing." - You don't need the comma.
"'Don't you know' He smiled slowly ..." - You need a question mark at the end of the speech.
" ...my couch,which also ..." - There is a space needed in here.
" In the end I went and plugged my laptop back in at my desk to charge ..." - I would take out "went and" because it adds extra, unnecessary words to the text. It is tighter to just say, "In the end, I plugged my laptop in."
This is just a description I wasn't sure about: Sam hearing the bookstore door "screeching" as it opens. I've never heard a door screech before, and it jumped out as an odd description.