Can the camshaft on a 2zz be replaced in the car?

I was able to do the test by removing the battery hold down and just sliding the battery aside. Easy fix.
In words, here's what happened. I can post the screen shots if you want.

Started car and immediately saw:
STFT = -6.3 LTFT = -26.6
After idling 3 minutes w/A.F.
STFT = -1.6 LTFT = -25 The STFT values varied +,+,- repeating. So up and down crossing zero.
At 2500 RPM after 3 minutes w/A.F. (did not restart tool. Probably should have)
STFT = -5.5 LTFT = -27.3 (the + then - crossings continued).

At startup w/o A.F. (tool restarted)
The idle started surging (going up and down), STFT always neg. and with larger values. Strangely LTFT got a little better.
STFT = 0.0 LTFT = -25.0
After idling 3 minutes w/o A.F.
STFT = -14.1 LTFT = -23.4
At 2500 RPM after 3 minute w/o A.F.
STFT = -3.1 LTFT = -20.3

The values were always changing and these are just snap shots. Generally the STFT with the filter were going from positive to negative over a small range (~ -3.6 to +5.5). Without the filter the trims were going from about -14 to -3 and the engine was always surging to some extent.

The air filter is a currently dirty but soon to be cleaned K&N and I verified that the MAF sensor is a new Toyota part.

Seems like the intake is definitely playing a part due to the surging issue. But what can happen in a simple tube other than resonance? I await your responses oh mechanical masters.

Looking at a static value of the MAF doesn't tell you much. If you want to test your MAF sensor and circuit with more detail, then do a third gear or fourth gear WOT run from as low an rpm as you can start all the way to red line. This means just get the car moving, put it in the chosen gear, then mash the pedal to the floor and keep it there, all the while logging MAF and rpm. The MAF versus RPM curve should look very much like the HP curve of your car that you would get from a dyno. You need fast logging to do this properly and it's possible you might get that with the Auterra. Back in the day I used to get pretty good road dyno plots with the Auterra. Nowadays for fast logging on a stock ECU I use Torque Pro running on Android with a OBDlink SX adapter - this is their fastest adapter it will max out the datarate on a K-line and it will give about 100 PID/sec on Can. Or you could do a road dyno run with your Auterra. Look for flat spots/dips in the HP curve. Anyway I would start by substituting a different MAF sensor and see if the problem persists.

Here's an example of a MAF versus RPM log I took with another car, comparing a slow-logging adapter with a fast logging adapter. I used this log to diagnose the variable intake actuator on the car. It also shows that a slow data rate adapter is useless. A static value is even more useless.

Ok, I checked all of the wiring regarding the MAF sensor and I mean all of it. I checked all five wires coming off the sensor and every location to which they went. I made sure to wiggle the wires while testing to make sure there was no intermittent contact. Four of the five went to the ECU, and the other one went to the EFI main relay, but there were also connections to the O2 sensors, fuses, relays, VSVs and a few other places. It all checked out.

I decided to just order a new MAF sensor. It's possible that this one ISN'T actually a new Toyota part. I checked my documentation and I don't show a new one purchased at Toyota, only one from a parts store. I might have done the check with the new parts store version, decided they were the same, and put the original one back in. Anyway, my local dealer's site is down, so I'll order it when it's up. I'm not going to do a junkyard one because the best junkyard for this is pretty far away. I'd rather just swap in a new part so I can be certain. I'll report back with what I find.

What do you guys think about the coolant temperature sensor as a cause? It always reads what I would expect on my scan tool and I'm pretty sure it's just a temperature sensitive resistor, but that could be a reason to run rich, I believe. Plus the car runs better when it's warm.

Ok, so it doesn't seem like the temperature sensor is a candidate, then. I might just have to order the Denso MAF Sensor as Toyota's site still isn't up and they can't tell me when it will be. Strangely, they are trying to push everyone to order online and then they don't keep the site up.

MerryFrankster, I appreciate all of your help on this, but I don't understand why you put the comment about the tricorder. Maybe you didn't intend it, but it sounds a little condescending. I don't believe I said anything about reading the sensor directly. If I wanted to do that, I would pull the sensor and measure hot water with it. I'm merely saying that I'm going from memory (which is always dangerous for me) and I seem to recall the temperatures were as expected, but I never looked at it specifically. For instance, check the temp on the live data, start the car and periodically look at the temp to see that it was climbing as the car warmed up, etc.

The MAF sensor finally arrived yesterday. I just put it in and ran the car without the air filter, since that is where the surging was worst. The surging is 80% better, but still there a little bit. The exhaust still smells strongly of gas even after warm up. I disconnected the battery to reset the fuel trims and the short term fuel trims were always negative. Between about -2% and -20%. When I held the throttle at 2500 RPM the fuel trims came closer to zero, but still almost always negative. When the long term fuel trim finally set, it was at -8.6%. Idle is still high even after warm up (1200 RPM).

So better, but not really fixed, I think.

Any other suggestions? I'm thinking about changing the plugs and then moving on to the fuel injectors. MWR provided me with brand new plugs, but I bought new Iridiums instead. Perhaps I should install the plugs from MWR. It's easy to do and can't hurt. Maybe I'm getting an incomplete burn instead of running rich.