Kia - Rio5 :: 2002 - Transmission Fluid Flush And Front End Rattling

I have a 2002 Kia Rio Cinco, (named Simple Jack) with about 150k miles on it, that I have been bringing back from the dead. I've replaced the shocks and struts, brakes, wheel hubs, wheel bearings, part of the brake line, the timing belt, motor mounts, fan, valve cover gasket (needs to be redone because my mechanic got sloppy), spark plugs & wires, windshield and wipers, and the radio. I sound proofed the interior, pulled the seats and carpet out and power washed them. I am also doing some body work on it. Normally, I am pretty good at troubleshooting the problems, but not-so-much doing the actual repairs. I tend to panic, and get paralyzed by the fear that I will break my car worse than it is.

The first was about doing a transmission fluid flush. I got the filter and the transmission fluid and while my ex-mechanic was breaking my car the last time, I asked if he could do the flush. He said he would not do it because the transmission was too old and it would break the transmission if he did it. Since the fluid looked dirty and probably had not been changed for a while, his logic was that the parts had a layer of dirt on them that would be flushed away with the fluid change. This would interfere in the operation of the transmission because the parts would no longer be able to make contact with each other.

At the time, this made sense to me. However, after some less than stellar repair attempts, I have some doubts as to the validity of his claim. So I am asking you all if this makes sense.

The second question is a problem with rattling. I had purchased the tie rod ends, front stabilizer and bushings for the suspension. I asked my mechanic to change all the parts when he did the front shocks and again I asked when he did the front wheel hubs. He said that I didn't need the crap. So my car has a weird rattling when I drive. It sounds like it comes from the top of the engine, but at speeds around 60mph, I have some vibration in the steering, too. I am concerned that something may be wrong with the steering or maybe it's just the alignment. However, I think the rattling may be independent from the vibration. I have not been able to determine the cause of this and my plan was to just keep replacing parts until it is fixed. I figured I will have a new car by the time I am done. What I can check next? Should I do the tie rod ends? The bushings? The CV joints? I know I need a new mechanic.