Some opinion, some fact....
1) Hesco does whatever you want them to do, so to me that is a great advantage. They set it up for either the 4.0 intake or the 4.2, and they told me that if I changed my mind, I could have the mounting studs moved in the future, so I liked the sound of that.
2) I'd say that having the head delivered with the water jackets filled, a new valve cover, valve cover gasket (the metal and rubber type- not cork), and really expensive head gasket (it's the metal kind, with several layers...the factory gasket is more like one layer with some kind of felt on it....the Hesco gasket is clearly a high-pro version). So if you add up all the trouble of getting the modifications done, and finding and buying the upgade parts, I'd say yeah, it is worth it. I got the thing in the mail and installed it. Bing bang boom. Add it all up and compare- you are still paying more, but for me it was paying to remove a headache. You do need to buy new head bolts for a 4.0, something else I mistakenly forgot in my excitement.
3) I used a weber carb, so not sure from you saying that you have a 4.0 intake if your intent is to do a full MPI swap, but I'll give you my experience whether it helps or not (might help someone): I maintained the factory pulse fuel pump, and I wish I hadn't. I had to use a fuel regulator, and the fuel lines go everywhere because of mounting locations, and I still have the hard fuel line that runs over the valve cover (which I hate), and the pressure gauge pulses, so my perfectionist self wishes that I had coughed up a couple bucks for an electric fuel pump for the weber, which I know is available.
Maybe someone else can answer this one for the MPI if that is your intent.