I would first check the basics before assuming the engine needs rebuilt. Ignition components that where worn before can quit working properly after an overheating conditions. It will take some time to check everything but worn ignition components can cause a knock sound.
A vacuum leak can cause a knocking sound. Check for this. I would also suggest doing a compression check. Cracked heads show up pretty quick. It will also give you an idea of other worn internal components that may need to be replaced should you have to rebuild it.
Main bearing wear can cause an knocking sound. Possible as well due to the hot thin oil.
As far as what needs to be replaced during a rebuild? You will not know tell you get in there. Components that may have ran fine in the running form may need to be replaced because the measure wrong (to worn) and you do not want to damage new components that have to be replaced on a rebuild.
So in other words we need to pull the engine apart and take a good hard long look at what we've got. My buddy drove the car a good 15 miles with rodknock until the oil filter clogged with metal. We'll be pulling the engine soon to do work on it.
Is this car Front Wheel Drive? Personally, if it were my car, I would not bother to rebuild a HT4100. I would stick in a 4.5 or 4.9. A 4.5/4.9 with under 100k miles can be bought for less than $400 on the used market and they made a lot of improvements to them such as the roller camshaft. These are long lasting engines and a 100k mile engine should still have a lot of life left.