Sounds like you could have several possible things.

When you say, "cracking noises from the engine" it makes me think of the catalytic converters. As for the CEL, you need to get the read out and see what it says.

Early model years seem to have a higher rate of transmission failure. I had a very easy 30,000 miles on my ML when the transmission had to be rebuilt.

It seems like the first thing you need to do is see a technician and get their assessment. Once you have a good idea about the problems, then try the search feature. Sometimes there are some inexpensive things to try, somtimes you just have to bite the bullet and pay for expensive repairs.