Context Brain, context. Not yerlling at you, just saying to take notice of the context. In the context of 4.0L SOHC Rangers, there were no flex fuel Rangers. The 3.0L really does not matter in that context and mentioning it adds confusion.
"a difference for the 4.0 sohc in fuel systems between 2003 and 2009? " May have been, but if you are swapping the long block, they are irrelevant. Remove the components from the existing long block and install on your new long block. Again, going into more detail adds confusion.
"Looking on doing an engine swap and just trying to find out if that's something I need to look out for. " Swap is a poor choice of words in this context. Swapoften conjures the notion of installiong a non-original engine. Something like installing a 3.0L, 5.0L, or LS in place of his factory 4.0L SOHC. This is a replacement, he's removing one 4.0L SOHC and installing another 4.0L SOHC. That is, unless he left out an important piece of info like his truck has a 2.3L or 3.0L.
He is not trying to install flex fuel. He's asking if there are any concerns with installing an engine from a flex fuel equipped vehicle into his non flex fuel truck. He won't be swapping ECUs or any of that stuff.
Changing ECU to one that includes Flex Fuel would open up a lot of issues, well beyond just the fuel system. Without going into depth, that would involve almost every computer on the truck due to the way they communicate with each other. Since that is not the plan and does not affect the engine itself, it's best to avoid those issues and avoid adding confusion.
The extent of the fuel system on the engine is fuel rail and injectors. He has a 2003, and according to RockAuto parts listing those injectors were used from 2001-2003. The listings show 2004 fuel injectors were 1 year only, and 2005-2010 being the same between all 4.0Ls. Main reason for the fuel rail to have changed was if the intake changed or fuel system style changed (return vs returnless) and I doubt the latter happened.
Considering that he is changing out the engine, it is only a few extra bolts to get at the fuel rail and injectors. Remove the 8 bolts holding the upper intake to the lower and the fuel rails are right there. If you need more room, the lower intake is another 12 bolts holding it to the heads. All of those connections use o-ring seals, so easy cleanup and prep for reinstallation. If I were pulling the entire engine, I'd be removing the upper intake anyway as part of the process just to get it out of the way and prevent damage.
No matter how he slices it, he will want to install his injectors and sensors onto the replacement long block to ensure compatibility. Engine accessories and mounts are going to come off anyway for removal and installation. There's a decent chance that the oil pan and exhaust manifolds will need to be moved over unless it's from another Ranger. I don't know about the upper intake, but they may have changed over the years and models as well.
In other words, just use the long block and maybe lower intake of they are the same. Move all of your existing stuff to the new longblock. You're going to be stripping the engine down that far for the change anyway.