Here's one of the big differences, and a possible reason to go with the earlier version.
This is a pic of the '95:
And this is a pic of the earlier style:
Note how there's an 'elbow' on the '95? Well, on the '89 style where it's at a right angle, if you turn the top part around so the air intake is on the driver's side, you can hook up your throttle linkage almost exactly like it's a carb. No muss, no fuss, no need to replace your gas pedal and put in a cable-pull setup.
AFAIK, you can't do that with the '95 version, because that elbow prevents you from being able to. It may be that the throttle body can bolt straight up without the elbow, similar to the earlier version, but I'm not sure. I do know that later versions were cast with a non-removable elbow, which removes even more options.
In addition, the distributor on the '95 is kind of a pain compared to the '89, but the real kicker is probably going to be where the dipstick is located. You might be able to get away with the factory side mount, because your truck has more clearance on the sides, but I'm not sure. I know it doesn't work for those of us with shock towers, because there's no room for it. The '95 block has no place to actually mount the dipstick in the timing cover. The '89-93 version hasn't got the boss for a dipstick, but at least it has a flat place where you can drill the hole and mount it if you want.
The old EEC-IV computer is also rather friendly to do engine swaps with. The ODBC1 used in '95 is a little more persnickity.
EDIT: The top pic is NOT a stock '95 manifold, but a GT40 style. My bad!! No wonder the snout's removable.