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First if this isn't safe to drive, have it towed to a shop to get it checked out. Some of the things I would want to check are what this feels like with the key off. I'd be looking for any mechanical failures, in the front as well as in the rear then address the steering issue from there.
The AC may require being discharged and lines may need to be disconnected, but no line should need to be cut unless the fittings have been damaged and cannot be taken apart as designed.
The catalyst monitor runs at several different speeds and engine loads on your Toyota. A trip of about 25 miles that includes some in-town stop and go driving, then rural highway for three to four miles (35-45mph) then interstate driving for about five miles (60-70mph), then back to rural highway (40-55mph) and then you can check for readiness, and or pending codes in case the test ran but didn't pass.
Diagnosing communication issues is something that is new for all of us. The right tool to use is an oscilloscope so that you can see the voltage on the data circuit over time. To communicate between the cars computers and the scan tool the signal has to rise above a specific voltage and drop below a specific voltage. If one of the computers has lost power, it alone would be missing from the network, but if one has lost its ground, it will back feed power to the data bus pushing the voltage high and disrupt the entire network. The factory scan tools also have additional functions built into them that assist technicians with diagnosing communication problems. You're going to need a specialist to help you with this problem.
You might need a new window regulator, the question would be whether it comes with the motor or not.
Have a shop check it out, explain the symptom for them and maybe if possible be available to go for a ride with the technician so that he/she gets to experience the sound with you.
Are both of the hoses to the heater core too hot to hold onto with the engine running and at full temperature? If not you might have an air pocket in the heater core or it may need flushed out or replaced.
What you need to do now is what you should have been dong all along and that is have a technician diagnose and attend to the problems correctly. Not fixing it completely and not using quality components makes it more difficult to diagnose what's wrong. In a lot of cases like this not only is the original failure still there, additional problems often get added on top of it either by the installation of questionable components or just because more things have been breaking and/or wearing out on the car. The biggest problem right now is that misfires ruin catalytic convertors, and there is no way to know from here without doing real testing if that is yet another part of the problem now or not.
Any slightly hooked pick tool can grab that clip and pull it from the window regulator. You have to make sure that the clip doesn't go flying and get lost that way. That's how we did it years ago before the clip tools ever showed up on the tool trucks. My original tool was a broken choke cable wire that I bent at a 90 degree angle (approx. 1/4" high)
Are you losing and having to add coolant? It could just be normal exhaust vapor condensing.