Howdy
You can take the rod and piston that measured 12 down, and install it in the number 1, then 4, then 5, then 8 cylinder and use it as a height gage. If it is 12 plus or minus 'x', you have a clue as to how square the block really is. Write it down, then have the machine shop use this data for guidance. I mike the dimension in all 4 corners with a FE tool and long calipers. I have a depth gage too. a real good FE machine shop can blueprint your compression height too. An average machine shop won't.
Then you know, if the deck is the issue, or the other assembly maybe out of tolerance for sure.
Now here is the wrinkle. If a crank grinder was sloppy, they may have turned the crank throws wrong. You can catch this but please note, if the crank is 10 or 20 under on the rod journals, it may no longer have the same exact stroke on each pair of rods. Seen that on a tear down measuring check. So you will get clues and can back check this too, before re machining it all.
If a crank is centered fast and dirty as the rod jounals get ground, they can be off 2,3,4 thousandths too. Check it out? using one rod and piston as a gage, sets the stage to check, then eye the true stroke.
I always re install any crank after VELASCO, BRYANT, CROWER, SCAT or SHAVERS stroke corrects it exactly, and then indexes it to be exactly 90 degrees apart on the throws. If you want free power, look in to this too. An we give the grinder the dimesion we need, after sizing the rods and mains, and measuring the bearings to the 0001 (tenth). This was, you set the mains and rods where you like them.
On the cam, FORD raced so many trucks, and we won so many races and championships with F250s, off road,,,,I would look back, then forward for fun. I would go to our old cam grinders for some nice cams too. We won a lot with FORD cams, and the below. Super reliable grinds too
An ISKY 262 Mega Hydraulic is on 108 lobe centers, and has a nice lope, and a bunch of grunt down stairs for a 390 with ported heads, and a Street master. Pull hard with headers, ported heads, lower gears, and a 780 or 750 DP Holly. It is 488 lift, 256/262 duration, 202/208 ex duration at 050. Also the 270 HL 510 510 lift, I like this extra lift here, over a 270 comp, 270/270....216 /216 at 050 lift. You have more choices there too. ISKY has never used the less durable core made in INDIA. Be careful there. If any cam company strongly suggests that you nitride a cam, look out. The core is not american probably
We ran ENGLES too, they make wonderful FE cams, and we won a lot with CROWER cams, like the Desert Dualer series and similar grinds to a 270 comp. The 270 Comp cam is a nice choice but don't forget many companies have old grinds. LUNATI is well known for many great FE cams too. CROWER has excellent FE cams in the 270 range and they were a vendor to FORD back then too. Full sponsor to Holman Moody Stroppe and key to many wins for Parnelli Jones and Walker Evans. ENGLE helped us win for FORD too.
On a Street truck, with manifolds, and the specs you chose, we also really liked the FORD, 6250 B cam. We called this the Cobra Jet B cam. Real nice piece for many FE's. It sounds true Ford to us too. Has a Detroit EEE lope. Wide lobe centers and excellent street manners, no power brake issues, etc.
Ford listed the CJ cam at 270°/290° 'gross' duration, lift as .481"/.490", and did not publish @ .050" specs. Crane & Lunati list their 'blueprint' cams for the 428CJ/390GT as having around 224°/232° @ .050", but the OEM cams really checked out around 209°-211°/219°-222°, depending on who was doing the measuring, and valve lift was more in the .475"/.486" range.
ISKY and LUNATI have a Blueprint series of the original FORD CJ cam that is a real nice 390-428 cam, with a mild lope, and it has the attitude that FORD engineered in for a heavy car on pump gas. CRANE has some real nice FE cams no doubt and they provided FORD with special FE grinds decades before COMP was born. No knock on Scooter and his fine guys.
We honestly won a lot more with dual pattern FE cams since the stock exhaust port has some issues to work around in some cases. We often opt for a grind, rarely a catalog cam, and I would check in to some dual pattern grinds too. FORD spec'd a dual pattern cam for the CJ Hi Po cams for good reason for example
The tight quench tricks are always a very wise investment as descibed
The tight piston to wall, combined with a torque plate hone is also free horsepower and durability
Blueprint the oil pump, check the end play and maybe shim the relief valve, add 1/4 NPT pipe plugs in place of the press in plugs, maybe relieve the block around the intake valves, and line hone it if needed. Chase all of your threads with a tap, debur it all a bit, balance it nice and have fun !
We always clean the ports up at least to the level of pocket porting, and we have porters here, or if you are patient, and have a plan, you can smooth up each port around the bowl, do a little port matching, cc them, we always do that, and more. Port them before you do the finish valve job or have one of our members do a basic street port job. I have very good head guys if you want a referral. I like to do it myself, for ever anyway, many here do it too. Ask around maybe.
Sounds like a fun build
Have a blast