Multiple misfires / repeated ignition coil failure, need help with some odd symptoms

Have an '06 with about 200k miles and having some issues. Bought it in 2012 with 30k; up to now all I've needed other than maintenance stuff (brakes once, etc.) is the inverter water pump two years ago, and an ignition coil last year. It also burns about two quarts of oil every six months.

Trying to figure out some issues I've been having. Last year I had a misfire which turned out to be a bad ignition coil. Might have had a mild misfire on a second cylinder, but was mainly on one. I changed all four plugs (official Toyota ones) and coils (Denso), which were the originals, and the problem stopped.

Fast forward a year to today and having the same issue again. Got codes scanned and they read as multiple misfire, one mild and one severe. Recommendation is to change the coil(s). I get the flashing check engine light.

Since the misfire began a few days ago I hadn't taken the car out on the highway. Yesterday I did, and speeds over 55mph or so (don't have a speedometer since combimeter is out) took the battery down to 1 bar once every five minutes or so. I'd need to pull over, recharge, rinse and repeat. I was in a rural area with no major roads running parallel, so getting off the highway wasn't really an option. Once I got back home, no real problems driving locally.

In addition to the dropping to one bar, I would get a 'skip' in the transmission/drivetrain. I've seen it described as a slip, but there's no delay and knock into gear like with a slipped trans, it feels more like I drove over a bump and it took the wheels a half-second to regain traction, but there was no bump in road.

I had the one-bar issue prior randomly prior to this, for about the last 6 months. I'd pull out of my driveway in the morning and go from two bars down to one, have to wait a couple minutes for ICE to recharge it, then resume driving, and no issues for rest of day. It never prevented me from driving normally on the highway and would happen maybe once a week, and there was none of the transmission skip.

The battery fan came on at one point while out on the highway. We had a hot last three days here, mid 90s. When I popped the hood the engine was running hot, not ultra hot but more than normal. Again though, was about 92 degrees. So just to summarize:

1) Ignition coil failed twice in one year/severe misfire has recurred
2) Battery draining to one bar at high speeds, have to pull over and recharge
3) Engine running somewhat hot, though was a hot day
4) Battery fan came on for a few minutes while on highway, don't recall hearing it recently
5) Transmission/drivetrain 'skips' while on highway, especially when battery drops to 2-3 bars
6) No real issues with non-highway driving

Is it possible that the misfires/general inefficiencies in the ICE would not allow it to keep up with the hybrid battery recharge at higher speeds, or does it simply look like a bad battery/bad modules at this point? Thoughts on the repeated coil failure?

I also have a coolant control valve code coming back also when I ran the codes. I was told by the official Prius tech at my dealer that this code can get triggered by the water pump and was in all likelihood an error, so I never changed it out. I did buy the CCV on Ebay before that though, and have it on hand (was cheap and didn't want to pay for return shipping). Coolant levels are near-full and I've never once changed the coolant since has never been low.

My tentative plan of action is to replace coils/plugs in respective cylinders tomorrow and see if that solves the misfire, then take it back out on the highway. Probably change out the coolant valve also. Also going to try the Torque Pro app to test the battery modules.

I have a spare hybrid battery from a rear-end damage Prius I bought for $1000 a few years ago on Copart, for the body panels and may swap in those modules (or might just buy new). I also have a spare engine and transmission from that vehicle with about 120k miles. The prior owner of the rear-ended car seemed to be meticulous with maintenance based on records in glove box. Engine ran very smooth when I picked car up.

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(Don't want to overload post further, but in addition to all this, for the last few months I've been getting the issue with the parking brake, where it says to use emergency brake on flat area. It's completely random and doesn't seem to be related to my driving. I have to park with emergency brake and turn car off. If I wait at least a few minutes, I can restart the car without issue. But if I need to restart it immediately, I have to pop the positive terminal off the rear 12v battery and put it back on, in order for it to allow me to restart. My hunch is that it's computer-related rather than being a mechanical issue with the 'pawl,' but not sure. The only thing I can do to cause this is hit the P button before the car is 100% at a full stop. But the warning screen will also come on in the middle of driving with no apparent cause. About 80% of the time I can use the P button normally, with no issues)