CPU heats up a lot and smells weird

The steps you followed so far are good.

At this time I personally wouldn't worry about the missing cap. You can decide to solder a new one on once you solve the overheating CPU which, like @oldturkey03 said is probably due to a short on a line leading in or out of the CPU or a component on the other side of the board. Another reason for this overheating could be that you used too much heat to remove the shields and caused a short under a chip or somewhere random. I've seen cases when solder "bleeding" from the anchors of the shields touch and short with a near by component. That simple.

As for the cleaning process, l would add ultrasonic cleaning if possible. An ISO baht (provided it is 99% pure and followed by good air drying) will chase the liquids from under the chips but not clean the crap well enough like a good sweep ultrasonic would.

I would also reflow dull or corroded joints and/or replace corroded components.

NOW, all the above being said, I wouldn't waste time to salvage a heavily damaged 5C because such a rework would be so lengthy that replacing the unit would probably be more economical. Unless this is done to salvage data.

Second, even if it works, your phone has now osteoporosis. All the joints that were corroded are now fragile and can fail at the slightest stress. Specially that 5C have a plastic shell and flex very easily.

There is a high probability that the phone will soon come back with touch issues, service issues, sound issues, to name a few. Customer would be unhappy paying a fee and getting a troublesome phone, and you would be unhappy putting so much work only to end up with an unhappy/ungrateful customer and possibly having to refund. Unless the liquid damage is really extremely limited, I wouldn't bother.