i havent done this swap myself but i have read several build threads, where they have used the sohc with a ohv computer, specifically "racin n' drummin" he has the first build thread that i read where someone swapped a sohc in. like i said he goes over the whole process in his build thread.
from what i remember reading the only thing it limits is your redline, because the ohv has a lower redline.
also, i dont remember if pats is a problem with later year engines. but i seem to remember reading that using a ohv computer eliminates that problem.
i have though long and hard about a sohc swap, but seeing as tho 5.0 explorers are a grand and a sohc in my area is a grand its a toss up. but the sohc has got basically the same hp of the 5.0 just a little less torque.
as far as obd1 running an obd2 system... the engines are the same asside from one being sohc and one ohv, thats why its still a plug and play swap, there was one thing i remember reading about that was a concern, because the ohv does not have it and the sohc does have it, but no body ever ran into any problems. so as long as your sohc sensors are good then there will be no check engine light.
theres some really good info on this on the explorer forums.
i assume since you can use the transmission on iether engine to go with the transmission parts for your engine, so sohc parts.