Ran through puddle, Runs normally at times but sputters most of the time

Up until running my car through a puddle on the highway,
my 24 year old Camry has run great. At 361,000 miles, it
starts up immediately and has been running normally and
quietly for the 21 years I've owned it. Aside from normal
wear and tear and replacement of parts that wore out, I've
never had any chronic issues with my car. I do as much of
my own maintenance as I'm comfortable doing. I did have
an issue where the cruise control didn't work for a few
years, but that fixed itself recently somehow. Also, my
reverse lights and high beams don't work, but I just live
without 'em. The day my car changed for the worse, I was
driving through heavy rainfall and ran through a deep
puddle on an exit going 45-50mph(the splash went higher
than my hood). About a mile later, my car started
sputtering, I lost acceleration power, and at times had no
response at all when trying to accelerate. 30-60 seconds
later, my car stalled. A nice guy pushed me to a gas station,
where I called a car savvy friend. He suggested taking out
the air filter to see if there was any water that might've
gone through the air inlet and also buying some starter
fluid to help the car start up again(if air filter was dry). After
removing the air filter, I found it to be totally dry, and the
area underneath the air filter was completely dry as well. I
also checked the oil and found it to have the same brown
color as normal. Before I bought the starter fluid, I tried up
to 10 times to start my engine. It would turn over but not
start up all the way. It felt like it wanted to start but
wouldn't. After an hour, I got it started back up and it ran
normally again. But, 10 minutes later, it stalled and wouldn't
do anything but turn over. That's when I bought the starter
fluid and sprayed some on the air filter and some in the air
hose going to the engine. After, repeated attempts to start
the engine, it started up but reverted back to sputtering,
lacking acceleration power, and wanting to stall. 10
minutes later, it started running normally again and I drove
it on the highway 10 miles without any abnormal engine
operation. For the five days following, it's started up and ran
just as it always has, with normal acceleration and the
engine sounding quiet again. Then, on the fifth day, it
reverted back to sputtering, lacking acceleration power, and
sometimes I couldn't drive any faster than 20mph. Upon
returning to my home, I opened the hood and found the
engine rocking a little (never saw that before, but my side
engine shock mount is very worn) and the sputtering noise
was very noticeable, most noticeable at the exhaust pipe. It
sounds like a Harley motorcycle but much softer. Just for
the heck of it, I removed the wire leads from the battery,
touched them together, and left it sitting for 20 minutes.
Then, I reconnected the battery, but that didn't change
anything. The car was still sputtering. I've been driving it
since then for a couple weeks. I'm in the process of getting
a new car. But, I'd like to get the car working normally again
if I can. It ran great up until I ran through that puddle. I've
run through many puddles in the past 21 years and never
had any problems. I'm thinking it might have to do with the
fact that the plastic cover on the bottom of my car has
come off and is no longer covering up the bottom of the
engine. I bought some spark plugs and spark plug wires,
but decided I might be wasting money if I install them and
it doesn't change anything. The car accelerates slowly at
first and then, after 5-10 seconds of accelerating, it will
suddenly revert back to accelerating like normal.
Sometimes it bounces back and forth between normal and
bad acceleration.