They look to be brackets that hold either parts of the harness or hoses out of the way of hot or moving parts on the engine. If you cant locate exactly where they go, look around for wires or hoses out of place or close to something they should be such as a source of heat or the fan, belt, ect. Might be part of what youre talking about with hoses for the valve cover. I always look for extra threaded holes on the motor or chassis and see if it would make sense if a bracket is needed there. Looks like you've done a ton of work under the hood. With that much of an overhaul, hoses or wiring may not end up in the exact spot it was before so its hard to identify where those pieces go. If all else fails, zip ties will keep wires out of the way.
Jeep and motor look really good BTW!
1996 Jeep Cherokee- Project-- Rusty's 8in long arm, SYE kit, Teraflex driveshaft, Cragar soft 8's 15x10 with 33x12.5 Firestone Destination MT's, Eaton Tru Trac in the front