If the shafts were worn, they should be replaced, since "rotating" them doesn't do anything, the area that's worn is still worn and there will be play in the rocker when it moves and you'll get both noise and additional wear. If the wear was significant and the cause of the noise, you won't get rid of it until you replace the shafts.
Take a look at these images:
https://dl.dropboxusercontent.com/u/464376/vehicles/1991 Explorer/Pictures/Valvetrain/P1020909.JPG
https://dl.dropboxusercontent.com/u/464376/vehicles/1991 Explorer/Pictures/Valvetrain/P1020910.JPG
As the shafts sit, the rockers ride on the whole diameter of the shaft but due to the lifters & valve springs, there's really only pressure on the bottom side. Lack of lubrication means that this is a wear point. Flipping the shafts over isn't ideal but it's a cost-effective fix. Early on when I got the Explorer, I had bought rocker arms. I got them before I knew you could buy assembled shafts from Delta. I didn't want to waste the parts I bought. Plus, it was a thought in the back of my mind that "renewing" the valvetrain might not fix the issue.
Did you inspect the lifters to see if any of them were collapsed or seized? If all of the lifters looked good and none were collapsed, stuck, or otherwise damaged, then you probably won't get any different result even with new lifters in there.
I did go over the lifters. 3 were missing or had broken cones. I did a fair amount of research on that part and it looks like those are just installation aids for the most part. Like the end caps on injectors. They're just there for protection/ease of installation. Anyway, they all slid in their bores easily and there was tension on both shafts as I torqued down the bolts. I don't know for sure if any were collapsed, I don't think they were but it's kind of hard to tell with them in the engine.
It takes a while in any engine for oil pressure to build up and for oil to flow throughout the engine and get into the small areas, but on the OHV 4.0L it takes even longer for oil to get were it really needs to go, like the wear areas between the pushrods and the lifters. There's a lot of oil splashing around rather than precise, well designed parts and passages that channel oil where it needs to go.
The BEST thing you can do is ALWAYS use 5W-30 oil (or a similar viscosity 0W-30), and never use thick oil.
I would NOT suggest EVER using anything in the oil, whether it's Seafoam or anything else.
If you want to 'clean' the parts and passages then a good quality oil is what you want. It can take a few oil changes, but with a good filter, it can work. Mobil 1 is pretty good, the Pennzoil Ultra / Pennzoil Platinum seems to be really good cleaning oil if you want to try that.
You may also try different brands and see if anything works to quiet the tick. There's plenty of vehicles where one brand of oil causes some noticable noise, and with another brand (in the same viscosity) the tick just isn't there.
I'm thinking that it is a flow/pressure problem up top. I know I have good oil pressure, I used a mechanical gauge to see. I think there's just varnish or crud caught in the lifters or around that area.
The engine is quiet when started but about 10-15 seconds in, when cold, it starts chattering and then starts to quiet down when halfway warm then totally quiet when warmed up.
To me, that says that the oil left in the lifters from the previous drive is still there but when that runs out or the cold oil coming up can't flow properly, they start getting noisy. Then when it warms up, the oil flows easily.
I've heard good things about the Pennzoil additive packs and will probably try that. I only got the Mobil 1 due to the coupon they're running. In my usage, the engine has only seen Valvoline MaxLife High Mileage 10w-30 (summer and feeble attempt at slowing oil leaks) and one jug of the Walmart SuperTech 5w-30, more as a flush when putting the engine back together. I used to use the Motorcraft FL-1A filters but bought a Wix 1515 for the current change.