First off, welcome. You came to the right place. Second, WOW, thats quite the list. Looks like you're gonna wear out the search function.

-Regarding the temp needle being pinned, the sensor for that is on the thermostat housing below the coolant fill cap. There are two sensors just below the cap, the temp gauge being the smaller/lower of the two. Maybe you just forgot to plug the connector back in after the swap??

-Your misfire could be a number of things, but a good practice is to work from the plugs up, plugs-wires-coil. I had a misfire from too much oil in the spark plug wells, which in turn killed my coil. Im sure you would've noticed oil in the wells changing the head. Search and you will find the testing procedure for the coil.

-Lastly, the discolored coolant. I would try a flush and refill. There is a drain bolt on the firewall side of the block, above the oil filter, between cylinders 1 and 2 i believe, that allows the block to fully drain. Remove that bolt, disconnect the lower radiator hose, and the thermostat housing and thermostat. Stick a hose in where the thermostat was, and run water through till clear. Then do the same to the radiator. If the rad is stock, it will have a drain cock on the lower passenger side. Button her back up, dont forget the drain bolt on the block, and see if that helps.

Hope some of this helps to knock some items off that list. Good luck.