Noisy Idle/Check Engine Light
 

Hello everyone,
I am the owner of a '97 4Runner, emerald green since 2000. She runs beautifully most of the time, but I've had a couple of major issues with her over the past couple of years.
First, the flywheel went on me and I had that replaced in '03. Then, in '04 the pinion shaft just suddenly ripped outta the rear differential and I had to have that replaced. I was told then by the transmission shop that it was probably a result of the flywheel being replaced; that is to say, the mechanic who fixed the flywheel problem may not have tightened all of the nuts and bolts enough somehow cause the pinion shaft to rip out of the differential the way that it did. Of all the people I've talked to about it. Noone has ever seen that kind of a thing happen, especially with Toyota models. There usually pretty much bullet-proof. That's why I bought Toyota in the first place.
Now I have another issue. Suddenly, about 4 months after the tranny work was done (outside of warranty period of 90days), I cranked the 4Runner up and she started to make a noise like a lawn mower, if you will. Very loud and the check engine light came on too. She still has torque, but I haven't moved her because I didn't want to make any bad matters worse with her. I was told by a bootlegger mechanic that it appears that the nut on the flywheel has come aloose and that need to be tightened. Someone please help!
I don't know what to do. I just wanna get to the bottom of what's ailing her...