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Well I think I must have something else going on. The plugs look fine and are gapped correctly. The TPS seems to be adjusted as close as I can get it and verified it with the fan trick. I adjusted the timing again and tried to adjust the idle screw but I couldn't get it to idle smooth. I guess I will have to bring it in to a Mazda dealer and see if they can find the culprit. Frankly I'm getting sick of fighting with it.

Spark plug leads? People have had new leads go bad before. If you take out each lead individually whilst the engine is running, they should make the engine run equally as rough as one another. If you take one lead out and not much difference is noticed, that's your problem.

Any update on your issues?

The only update I have is last week I ran a scan tool on it and it is running lean on both banks. The hesitation is still there along with the rough idle. I have not been able to track it down.

You've done all the hard work. You're just missing something simple. Look for an air intake leak. You likely are getting air into the engine that is not being measured by the VAF. That will cause high idle, lean condition, hesitation, etc. So somewhere between the VAF and the intake manifold air is getting into the engine, but the ECU can't account for it and adjust. Possible suspects:
Air intake tube and connectors
throttle body gasket
intake manifold gasket
leak between throttle body and idle air controller (cylinder on bottom of TB)

or maybe you have a bad VAF

I'm fairly certain my intake tube/connectors are all good as I replaced the entire tube. I know the throttle body gasket is good as it was brand new when I removed the body/IAC for cleaning. My new suspect may be the manifold gasket. I only think this because the guy who rebuilt the motor didn't install the valve cover gaskets as he should have so maybe he did the same with the intake manifold. Is there any good ways to test without removing the manifold?

if the previous owner did a crap job, there's a good chance he most likely reused old gaskets. Unfortunately you will need to remove the im and get a new gasket set for it. Whilst you take that off, you will be able to check other things for leaks more thoroughly.

It's unlikely to be a sensor causing lean conditions. When they go bad, the ecu runs rich for safety not lean.

How lean is lean though? Like 20 to 1?

Sadly I can't blame a previous owner as I have owned it for the past 11 years. The crappy rebuild is thanks to a local shop that does machining and rebuilding. I guess I'll have to do some checking. I actually have it up for sale since I've pretty much ran out of money trying to track down the issues. Thought someone else could get a great deal and with some fine tuning have a great car. I guess I'll have to wait and see what happens.