Hi Bigearl!
What you're seeing is most likely a symptom of a lack of timely maintenance concerning oil changeouts or use of a poorer grade of engine oil or a combination of both......not so much 1 bank is running slightly hotter than the other (even though this can also be true due to several factors causing 1 bank to flow more airmass thru it--thus heat up more--than the other, but is also a normal occurrence w\ a V-engine design anyway--especially w\ 1 that is using 2 camshafts w\ VCT cam phasing capability--so isn't usually a factor).
This engine's
PCV system design is what sets up what you're seeing. Fresh clean air from CAI downstream of the MAF section but just in front of the TB is drawn into the B1 valve cover which then flows thru B1 CH oil drain passages\front timing cover area (this is why B1 side usually looks clean....) thru CC area mixing w\ the cyl blowby gasses from pistons\cyls, then back up into B2 side thru B2 CH oil drain passages\front timing cover area then enters the PCV baffle entrance at back of B2 valve cover at #8 cyl (this is why this side is usually a different shade of darker "color" than B1 side) then thru PCV valve then out of B2 valve cover into IM after TB (intake manifold vacuum created by deltaP across TB is what creates the PCV airflow movement). This air flow thru B2 is also much hotter than the air flow through B1 which will also lend to varnish\sludge formation in B2 side vs B1 side as well.
In OEM trim, these engines are designed to run on the warm side for emissions\CAFE stds purposes (low to mid 2xx*F range) which can put some load on engine oil to hold up w\o breakdown......thus why timely service maintenance & a good quality engine oil is a necessity to prevent what you're seeing in this Ford Modular 4.6L V8 engine of yours.
If good quality engine oil (at least the OEM Ford 5W-20 "blend" but 5W-20 full synthetic is better.......or IMHO 5W-30 full synthetic is all around best) & proper maintenance scheduled service changeouts are maintained, you should never see any signs of sludge depositing anywhere in B2 side period.....you might see some slight decolorization in B2 vs B1 due to varnish deposits forming but even this should be slight if good quality oil was used & strict maintenance changeout schedules are kept up. You also should NEVER see ANY type of metal pitting\fatigue either.......this is a good indicator of lack of oil changeout servicing as for metal pitting to occur, the blowby infused oil sludge is caustic which means that the oil had already started breaking down & mixed w\ some raw fuel along w\ moisture from the fresh air created an acidic mix that started attacking the ferrous (iron-containing) components......the several yrs this engine was in storage w\ this inside didn't help as well.
So just check everything over closely to determine if something can be safely reused or needs replacing. Those CH's & engine block could use a good cleaning in a chemical bath & properly blown out to ensure that all of the sludge\varnish is removed & all passages are fully clean & open.
You'll have to decide in the end as to what is acceptable or not to reuse\replace.........your dime, not mine.
Hope this helps.
PS-- Here are some pictures of my engine's CH's w\ valve covers removed for reference:
View attachment 88452 View attachment 88453
On the left is B1, on the right is B2. If a good quality engine oil is used along w\ proper, timely oil changeout servicing is done......what you see here is what you should see.....note B2 CH is almost as clean as B1 CH.....this engine had 152,800+ mi on her at the time of these pictures (taken when I was changing out the VCT solenoids & I found the broken cam follower on intake valve on #7 cyl in B2)...........
FYI.................