Never tried flipping the rail, but I would advise trial fitting the upper intake before committing to that course.  I'm not saying it will interfere, but it might and it would suck to get the lines all laid out to find a problem like that while you're trying to button the whole thing up. 

Another option may be to see what layout the factory fuel rails had on other 5.0 engines.  They ran that engine in trucks too for example, and if I remember right the air intake was on the LH side instead of the RH side on a truck.  This may have necessitated a different fuel rail due to upper intake interference.  Again, I can't say for sure, but its worth doing some Googling. 

I have read a few items regarding the explorer fuel rail, too. Looks like a nice option.  Part of the equation is what you are doing for fuel feed.  How and where are you going to feed fuel at the high pressure?  Edelbrock has a compact sump unit you can mount under the hood, and use a stock mechanical fuel pump to fill the sump, and it has a submersed HP pump that feeds a short run to the fuel rail.  Looks pricey, but I bet something similar could be fabbed.

Have you seen JamesW's website?

tubo, I don't want to rotate the intake itself, just get the fuel-lines to exit to the rear since that looks like the most direct route.  As an aside, I found the little aluminum spacers to replace the egr throttle bracket mount are $50+ which seems a little ridiculous.  Don't see any purpose other than to hold the bracket and not seeing any other off the shelf solution.

timc, Definitely familiar with the midnight designs website, but didn't know it by his name.  I plan to run both lines to the rear.

If the stock rails can be rotated the regulator would be under the intake and no idea if it would work, thats what I first thought was in the picture, but you can see the regulator top right.

I have searched e-bay completed listings for "(302, 5.0) fuel rail" and the only rails I have found that exit to the rear and keep the regulator in the same place is the explorer one.  They have sold in the past for $30-40.

The '89 and '90 engines would be the same.  The '93 Cobra intake is the same as the Cobra intake sold through FRPP, and is also interally identical to the GT40 intake also sold through FRPP and used on first gen Lightning trucks.  The GT40 is basically a tubular upper version of the Cobra, which is cast.  Remember if you run #24 injectors you also need to run a mass air calibrated for #24s.  Cobras ran a unique setup where they retained a #19 calibrated mass air, but ran #24 injectors, and the ECU was programmed to allow this and fuel accordingly.  If you try to run that setup without a Cobra ECU it will not run right.  The Cobra ECUs are rare and probably demand a premium becuase of the Cobra name.  Its best just to run a regular ECU and run the right mass air meter for your injectors. 

The mechanical pump to sump to high pressure system is interesting.  Its like how the GM 6.2 Diesel worked.  They used a block mounted lift pump to feed the high pressure injection pump that stepped up the pressure to injection pressure.  More complexity there though, and each additional part is a part that can potentially fail. 

Yes, the rails will work with any stock style injector, which go up to at least #42s.

The F150 rails may well be different than the Explorer rails in '96, because at that point I believe the Explorer was still being built on the Ranger platform, making it and the F150 substaintially different. 

The EGR spacer between the throttle body and the intake serves a purpose, even without the EGR.  The spacer has coolant flowing through it.  It was once common practice to plug the coolant lines and leave the spacer dry.  Without getting into a log explanation; don't do that.  Its beneficial to have the coolant circulating through there.  People used to claim it cost power due to the heat it added.  Fact is it does the opposite.