Toyota Repair: 1993 Previa LE 2wd jerking/loss of power question, throttle position sensor, valve cover gasket

Question
Ok, so I have a 1993 Toyota Previa LE 2wd automatic van, with 186,000 miles, and over the past year it has gone from the normal gear hunting from around 47-60 mph, and morphed into a rough idle. The idle is so bad that it can pretty much just stall when you are standing at a light. It will start to drag itself down, as if there is a load on the engine, and then most of the time it seems like it adds gas to the engine by itself, thereby saving itself, or the rest of the time it stalls (rarely but still). I have searched online for an answer, and it was suggested that a new Throttle Position sensor would cure the gear hunting (which has been going on for 4 years, but we have gotten around it) and the people at the Toyota dealership in town have suggested taking a look at the air pipes going into the throttle for cracks, since they said it could cause a "lean condition." A few days ago, I finally replaced the TPS, and it seems to of have fixed the idling problem, but the gear hunting still exists, but a lot less of a nuisance, and the car is still jerking.
Now this is the main thing that I don't understand. It seems like the engine has a problem with it's timing, since when I accelerate, it will throttle up, then suddenly lose power/acceleration, make a squeak-squeak sound, and sharply continue accelerating, which jerks the car. Is this because the valves need to be adjusted? or the timing?
The valve cover gasket is leaking, so I plan on replacing the plugs (have been in there for over 60k miles), and the gasket, and potentially performing a valve adjustment. I have already replaced the distributor rotor and cap since they were pretty much burned, so this is kind of my last-hope before it goes to the shop...
I kind of want to note that there have been some moments where I have not been overly kind to the car, especially when I have pushed it a few times to its top limit of 110 mph... in which case I burned the transmission oil the third time, and I am not sure if the Torque converter could be bad. My dad has forgotten to change the transmission oil twice, so for 2 times it has gone on 30k mile intervals. There is another problem here, since when the car is cold, you can place it into drive, then press the accelerator, and the engine rpm goes up, and the car goes nowhere, because it is not engaged to the transmission, when it is in DRIVE!! Do you have any idea what gives with this?
It is really rare when it happens, but sometimes I'm scared that I will pull into the middle of a particular intersection, and it will cut-out, and Ill get T-boned by another driver going 55mph... I apologize for the long story, but may I have your expertise on the matter(s)??

Many Thanks,
Dominic

Answer
It seems a while back there was a problem with the wiring from the throttle position sensor to the wire harness, some of the wires would break inside the insulation and cause shifting problems, check those wires and if any of will seperate from the sensor when pulled on them, this used to be a common problem, if any broken wires are found solder new pieces of wire in.
The transmission issue may be related as well so check the wiring first and then change the fluid.