There are positively located seals that fit an FE guide, but they are pretty big and depend on valve spring choice and retainer to guide clearance.  US Seal sells by dimension, but here is an example from another source. 

https://alexsparts.com/3-8-x-625-660-viton-valve-seals-flex-body-type-fe-ford-universal-vss-407-set-of-sixteen/

I agree though, good guides first, then if doing a valve job anyway, put real guides in (consider a 11/32 valve), cut the locator pad off and run a real locator and a nice Viton .531 seal.

If the heads are nice, you could just pull them down and cut the existing guide, but sometimes you will have retainer to seal clearance

As far as which brand of seal, I really like Manley Viton, Brent turned me on to them many years ago.  They push on easier, hold tight and last well.  It's all I really use now

Any play in the pinion? Does the yoke have cap locating tabs or need u-joint clips?

If the only thing changed is the center section, I'd be hard pressed to blame the driveshaft

Contact landlproducts.com

They make a swap kit, it's not cheap at 2100 dollars, but comes with a lot of good stuff for a bolt in.

I used one many years ago on a 73, not a bump but it worked great

This was a fun one, admittedly a lot of work fixing some odd things from a prior Cleveland specialist, but in the end a lot of fun and turned out very happy and healthy.  We made a number of runs, all hitting 7K and was happy all morning.  Pump gas and not a ton of overlap will make it very happy in a street Mustang with a Tremec

Performance Summary:
      Cubic Inches:  410            Dyno brand: Stuska
      Power Adder:  N/A             Where dyno'd:  Dale Meers Racing, Buffalo, KY
      Peak Horsepower:  582 @ 6200
      Peak Torque:  548 @ 4800


Engine Specifications:
   Block brand, material, finished bore size, other notes: 72 4 bolt main iron 351C, 4.040 bore, CnC squared, aligned, torque plate honed
     
   Crankshaft brand, cast or forged, stroke, journal size: SCAT forged steel, internal balance, 4.00 stroke
     
   Connecting Rods brand, material, center to center distance, end sizes, bolts:  SCAT H beam 6.00

   Piston brand, material (caster, hypereutectic or forged), dish/dome volume, static CR: DSS pistons, -18cc dish, 10.0:1

   Main Bearings, Rod Bearings, Cam Bearings brand and size:  SYandard Clevite rod and main bearings, Durabond cam bearings

   Piston rings brand, size, other notes: Total Seal 1.2mm stainless top, 1.2mm #2, 3.0mm standard tension oil ring

   Oil Pump, pickup, and drive:  Melling M-84AHV, ARP drive, Milodon pickup

   Oil pan, windage tray, oil filter adapter:  Milodon T-pan

   Camshaft brand, type (hyd/solid, flat tappet or roller), lift and duration (adv and @.050"):  Custom Bullock's Hydraulic Roller, 235 @ .050, 114 LSA on 107
   
   Lifters brand, type:  Morel standard travel hydraulic roller

   Timing chain and timing cover: Cloyes 9 position, factory timing cover

   Cylinder heads brand, material, port and chamber information:  SVO NASCAR B351, ported 225  cc intake, ported exhaust

   Valve springs: Comp 20655 Beehive
 
   Rocker arm brand, type (adjustable or non-adj), material, ratio:  Jesel 1.75 ratio, pinned

   Rocker shafts and stands, brand, material:  N/A
   Pushrods brand, type, length:  factory

   Valve covers, brand, type:   Unknown fabricated

   Distributor brand, advance curve information:  MSD large cap, 34 degrees total

   Harmonic balancer brand:  Unknown aftermarket

   Water pump brand, type (mechanical or electric):   Unknown stock replacement,  electric powered on dyno

   Intake manifold brand, material, porting information:  Roush SVO   single plane

   Carburetor(s) brand, type:  Dyno'd with 950 QFT and super sucker - 582 HP, customer 830 and no spacer - 572 HP

   Exhaust manifolds or headers brand, type:  Dyno headers

As far as the quench discussion, glad to see no attempt to make it too tight.  I think for most .040-.050 is plenty for the squish benefit, and I regularly run them proud with a 8554 and some even taller if we are trying to keep intake dimensions on the rare stuff.  Even comparing .045 or so to .036 I'd expect no gain and only added risk.

In terms of the machining, geez Howie, Brent was right, said Ford was all over the place, and then you come back with Ford couldn't hold a spec with their tech at the time, that is EXACTLY the point.   Who cares what the spec is if the machine can't hold it anyway?  Brent didn't say that the machinists were evil or FOMOCO was playing a trick on us.  I'll add that valve centerline, bore centers, cam bore dimensions are all over the place too once you start measuring.

Additionally, no doubt things flex with heat cycles, I am not sure what you mean by massive flexing, I don't agree with that, an FE is pretty forgiving on head gaskets even fewer head bolts than modern engines.  Although anything can move, they don't change .026 from end to end and grow .010 over deck height.  That's a crank centerline or deck machining issue that causes that much variance, and the numbers can tell you which it was.

Square deck a block or two, you'll see things, square deck 20, you can really see the trends.

Agree with all your points Ross but one sticks out to me. Sticky lifter bores. Having done long ago a number of in-car cam swaps, we noticed that the removed lifters had deposits on the lower (cam side) ends. Taking out the lifters showed similar crud inside the bores, hard to remove even with determined cleaning. We noted that some of the new lifters had trouble spinning in the bores. We went back in with lacquer thinner, acetone and even gasoline until the lifters spun easily.

Yes, if they can't spin, the lobes will go flat in a hurry.

Amen, and so easy to diagnose, if they don't slide in nicely, stop LOL

I second the motion from the gentleman from KY.

Lots of build failures that blame cam and lifters when they are the effect you see, not the cause