The 990937 filter in the picture is the trans. filter the other(990936 clark #) is the engine oil filter.
The two handles were probably used for accesory hydraulics like a side shifter and some other option maybe the truck had a clamp of some sort on it that rotated.
As for jacking up a truck is BEST to jack it up from the side,jacking by the counterweight although am sure is done alot isnt reccommended especially if the counterweight bolt is loose or missing.
The cap in the one picture is for fuel filling(gas/diesel) for the engine, the hydraulic tank should be on the other side of the truck,the hydraulic cap should have a breather on top of it and the dipstick attached to it.