well i am not around much but there are many here, just be patient.
the headers i refer to are shorty style. the stock or upgrade sn95 stuff cut and modded at the flange or the 351 swap style like shown here...
in 95 when i first converted my main truck i used the swap headers on the market that were long/mid length designs that actually required frame trimming...i did this for performance reasons with a efi cobra engine and they were flat flange gasket style....i hate those leaking pos...not for a abused 4x4 application, it was a bad move but there wasnt much else out there and information in the 80's and 90's was not quite so easy to come by like it is today..and we usually used k or maverick type manifolds or van manifolds on one side and the car type on the other from 88-93 or so as a standard..or at least the group i ran with...
so i had to hack the hell out of my frame initially...you wont have to do it so bad...you can actually just roll it a little ways to use them and clearance the drivers side a bit. no hackage

so the frame wont be weakened. of course mine is beefed up and wrapped with 10 or 14 gauge after i busted it jumping it like a rabid kangaroo.
and the aerostar linkage, this has been a staple since the mid 90's...
there is an early and later style...but you can forage jeeps and and vehicle you want with the joints and shafts you like and adapt them to your liking.
the cruise you just leave as is and make sure the vss circuit stays intact along with the body wiring..of course the brake pedel/power unit needs the vacuum line source for apply and dump if you have the vac style dump, and iirc you do. i went to gm style cruise...but i also have a 4l80 trans and diesel in my ranger...so i dont remember exactly what i had with the small block ford...i do remember some changes from 88-89 but i dont think it is an issue with your situation..there are several styles of cruise across the ranger generations. but if you keep it all you should be good.
that is why i suggest the system approach to the clutch situation. if the fullsize trans is set up hydro it is usually best to keep it the same...the master and slaves likely have different volumes and its is possible they wont get along too well. you can adapt the ends, i dont remember if the mater side is the same on those...possible just push the roll pin and pop the line on. i would have to see the actual parts in play to make the call.
the fuel pump...up to you. it is done regularly. a good pressure regulator close to the tank or in the tank would be my preference. but a
GOOD pressure regulator will cost more then a stock low pressure pump.