I don't think Tom was made aware of the problems prior to receiving the e-mail at home from Arthur Kahn on Monday morning. Near the end of the movie, Tom views a video link conversation between Meredith and Arthur Kahn that suggests the two of the them were keeping production problems from Tom. Arthur said that Tom was smart and would figure it out. Meredith's response was that Tom would be gone by Tuesday! She had already planned on getting him out of the picture so that her secrets (cost-cutting at the Malaysian plant) wouldn't be discovered. She would probably blame that all on Tom. Stephanie Kaplan, Tom's new boss at the end of the movie, realized that Meredith's operational changes were to blame for the problems with the Arcamax products rolling off the line. She wasn't going to hold that against Tom.
Garvin was blinded by the $100 million check he was about to receive as a result of the merger. He shows no loyalty to anybody that may get in the way of Conley-White signing on the dotted line. The movie doesn't suggest that Garvin conspires against Tom prior to the Tuesday meeting when Phil Blackburn tells Garvin that Tom plans to file a sexual harrassment suit. He seems surprised and he wants to act irrationally (Fire Tom!). When Blackburn finally calms him down, Garvin says that he wants it resolved quickly and quietly. When it is revealed (on Thursday, I think) that Meredith was the aggressor in their sexual encounter, according to Meredith, it is Garvin and Phil that come up with the idea that Tom could be fired for incompetence. This way Meredith could still carry on as the head of the spun-off division. Conley-White is comfortable with her. According to Garvin, Meredith saved the deal by suggesting the spin off. Garvin stuck behind her right up until the end when Tom exposed Meredith in front of DigiCom shareholders.
Meredith could always blame Tom for the disappearance of the Malaysian Operations files after he was fired for incompetence.
I just started reading the book. Perhaps some of these seemingly-unconnected dots are connected much better in the book?

The end of the movie was feel-good for "wrap it up quickly"'s sake. I didn't find it a satisfying resolution to the story as presented.
Yep. I thought the first half of the movie was stellar. Strong acting and good build up. But the ending really felt like a let down. Demi Moore gets owned twice because he had the evidence. What this movie tells us is that once a woman has you by the balls, you are basically beep unless you happened to have a recording of the entire incident.

Well remember, he was being lied to by the people at the plant and that if they had followed his specs and plans, none of the problems would have happened. This plant was in Malaysia, so it's not as if he could keep checking for himself, and he was already trying to investigate the problems he was getting before the events of the film started.
As for the other two moments.
1). Thanks to Garvin and Meredith, or Meredith on her own, the company had committed fraud. The damage to the company's cred had already been done and was going to come out at some point, the only question was who was going to get the blame. Now, if you can pin all that blame on a person that you have already gotten rid of, especially if you can paint him as a womanising creep who was too busy harassing poor innocent career women to concentrate on his job, then you not only get to dodge the responsibility, but you get to point out that you have already dealt with the source of the problem before knowledge of it came out. Hell, you could even get a bit of free publicity from feminists who want to promote the idea that tackling sexual harassment helps productivity in the workplace.
Remember that Garvin's daughter had died and he desperately wanted Meredith to have the chance his daughter did not. He probably doesn't even see Meredith's crimes as all that bad, because he's probably done far worse himself and perhaps even thinks that Meredith's amorality proves that she has the ruthlessness to succeed in a man's world.
2). If their plan is successful, they'll say that Tom was the one that wiped the messages to cover his tracks. Remember, in their version of events Tom is an incompetent who promised things he couldnt deliver, cut corners to make it work and then deleted evidence to cover his tracks. Admittedly, there will be logs that Meredith was the one who deleted the files, but if Meredith deletes the logs too, then there wont be anything that will suggest otherwise. Again, Tom is the problem, not the software or anybody else.