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@allmyEXes - The OTC 6488 tool is for timing the cams. The cams are the only thing that needs to be timed to the crank shaft with the tool, because there are no timing marks on the cams/cam gears. If you have a balance shaft on your engine (the 4WD engines typically have the balance shaft, but my 2WD '01 Job II 4.0L SOHC ST engine had the balance shaft) there is a procedure you must follow to make sure the balance shaft is set properly, but doing this does not require a special tool and the jack-shaft does not require timing. Please watch the fordtechmakuloco YouTube videos (most likely on #3 and #4 of the 4-part series) on cam timing and balance shaft timing.
Re the balance shaft, if so equipped:
Many people do not reinstall/replace the balance shaft chain when doing the timing chains. This is because most feel that it's not really necessary and the balance shaft, its chain tensioner and guide can be problematic. I do not plan to hook up my balance shaft chain and some here have even reported cutting the chain to eliminate it.
@swshawaii and @koda2000 .Do either of you own the tool set? I cut my balance shaft chain with bolt cutters. The tensioner was broken and inaccessible with the engine still in the vehicle. Also I didn't disturb the jackshaft and chain. I left it in time along with the right hand cam chain.
I haven't acquired the 6488 tool set yet. I'm waiting until I get my heads assessed before spending the money on the tool. I was temped to buy a pre-owned, never used OTC 6488 set I saw on eBay last week for $160 shipped, but I'll wait until I actually need it. After using the set I plan to resell it, as I promise you I will never use it again.