rough @ idle and acceleration after Throttle body cleaning.....!

Are any warning lights on?? If so pls take a sharp photo and post.

That probably is the brake actuator pump which runs from time to time. You can force the pump to run by repeatedly depressing the brake pedal.

The fuel pump is located within the fuel tank.

 

Since the check engine light is on, a DTC will have been logged. If DTC P0505 has been logged again, look for a vacuum leak such as a loose PCV hose, missing engine oil dipstick, or a loose / missing engine oil cap.

If there are no vacuum leaks, then since the throttle body was already cleaned, your mechanic may suggest replacement of the throttle motor. That would be a reasonable next step.

 

Did it rain in your area the other night and if so was the Prius parked outside?

Maybe some water got into one or more spark plug wells, thus causing the sudden engine misfire.

 

Have your mechanic closely inspect the plug boots for signs of arcing.

 

I apologize for this long post, but you had a lot of things done at one time.
If you're not the original owner, the first thing I'd do is got to www.toyota.com/owners/web/pages/resources/recalls
Plug in your VIN and see what recalls have been done and which are outstanding. Check the inverter water pump status. There was a Limited Service Campaign (A0N) to replace them on 2004-2007 Prius. See later in post.
P0505 is an idle Control System Malfunction, so one guess is around the throttle body.
Since so many things were probably disconnected to clean the throttle body, and it was good for 3 weeks, I'd check the following things, related to each thing you mentioned, to make sure they're reconnected right:
Make sure the PCV hose is connected correctly on both ends and nothing else was dislodged. It's a tight fit. I replaced mine at 110,000 miles. It was still good, but if you have it off and you have a $12 part you replace it.

THIS NEXT ONE IS THE BEST CANDIDATE FOR ROUGH ENGINE RUNNING!!! THE CE LIGHT DOES COME ON.
P1320 - Ignition Coil No. 5 harness is open or shorted
- Ignition Coil No. 5 circuit poor electrical connection
- Faulty Ignition Coil No. 5
- Faulty Engine Control Module (ECM)
so check the ignition coils and harness. If he disconnected and moved them to do the PCV, he may have either damaged something or a connection is loose.

As far as the throttle body cleaning, check these:
Check the MAF Meter to make sure no contamination got into it when the guy was cleaning your throttle body. It is very sensitive to contamination in its air gap. DTCs for the MAF are P0101-P0103.
It's a longshot, but a dying 12-volt battery can affect the MAF communication with the ECM too and many other things.
Also check the MAF Connector Wire Harness,
No. 2 Ventilation Hose,
No. 1 Fuel Vapor Feed Hose,
Throttle Control Motor Connector,
Throttle Position Sensor Connector. All those things attach to the throttle body and may not have been securely reattached.

Since he replaced the mechanical engine water pump, Prius gets air lock easily. Check your engine coolant level. Turn the heater temp to high and let the engine warm up until the thermostat opens (If it will run). Let it cool down, then check the coolant level, not just in the reserve tank, take the radiator support cover off and check in the radiator cap. If it's low, open the 6mm hex bleed valve in the opening on the opposite top end of radiator and add until coolant comes out, squeezing the radiator hose as you're filling. Prius is a bear to bleed the engine coolant.

The whirring could be your inverter or inverter water pump. The engine coolant and inverter coolant are separate systems in the radiator. The engine coolant is in the upper 2/3 and the inverter coolant in the lower 1/3.
The inverter water pump, if it wasn't already replaced under the LSC A0N, could be going bad. The transaxle/inverter also has the Automatic Transmission Fluid for your car. At 95,000, you're due to replace both inverter ATF and coolant. Use only Toyota Super Long Life Coolant and ATF WS. Both the inverter coolant and ATF are pretty simple procedures if you're a do-it-yourselfer. Lots of videos out there. Watch a couple and find one that looks like he knows what he's doing.

 

Another question about the oil in "cylinder #1 you mentioned. Was it just in the plug well or was the plug itself fouled with oil from oil actually in the cylinder? Is it back now that the rough running started again. I thinking if it was a quick fix it was just in the plug well, but someone had to be really careless to get oil in there adding oil and the dipstick is not even close. Oil leaking into the cylinder itself could cause those rough running symptoms and may be a deeper problem with seals or head gasket. I'm not that experienced in that area with Prius, so someone who is should chime in. I know on my son's old Accord there were oil seals on top and also on the bottom side of the rocker assembly that had gone bad at 160,000 miles. and allowed oil into the plug wells, but from the diagrams I don't see any such seals in the Prius.

 

Couple of posters found hairline cracks in the ignitor boots. Really hard to see apparently.Have to pull on the boot and stretch it to see.
8 year old car not unreasonable to replace all the ignitor boots. Misfires are tough. Usually ignition on this car. Doubt its the TB.

Btw, I believe there is a tsb out for your year concerning replacement of the water dam gasket. The seal/gasket that prevents water from overflowing the dam at the bottom of the windshield and dripping onto the cylinder head and getting in the sparkplug wells and shorting out the plug.
It consists of a new gasket and sealant. Search around.

Lusciousgarage.com discusses it on there many blogs.

 

The whole ignitor must be replaced. The boot and ignitor are an assembly.
Check Champion online.

I do know if I had to replace them I would only use genuine Toyota parts not parts store boots.

 

$79 each online. Thats the entire ignitor & boot assy. You may have a bad ignitor too.

Only way to really check this is to see which cyl is misfiring with TS and then move that ignitor to another cyl and see if it moves with it.
But thats alot of work and time. Like I said not unreasonable to replace them all at your year anyway.

Could have a cracked intake mani. Car ever been in a front end accident?