Your Balancer should be zero so no problem changing it as long as the new is zero.  your 428 was externally balanced at the fly wheel and a reputable shop would make minor tweeking adjustments internally.  You should ask your shop how they did it.
The Super CJ 428 had the hatchet weight behind the balancer to compensate for the extra weight of the LeMans rods

 I didn't like the way Hex head bolt seated either and a wrench or socket didn't get in there to well either, so I used Allen Head cap screws.  They seat a lot better on the spot faces from Lakewood

How about if you were to broach a keyway in the lifter bores, say a 1/8” x 1/16” deep.  I don’t have a bare block to see how high the oil gets before the drain back holes take effect.  I realize that it would not be under pressure and cold oil might not get there as fast…..   Just a thought

Cam Thrust plate and bolts and other FE stuff

http://stores.precisionoilpumps.com/valvetrain/

Good guy to deal with

We have some engine builders here that will most likely point you in the right direction

You'll have Welsh Plugs for your Oil Galleys. You can replace some with 1/4" NPT plugs but not all, so my opinion, just replace them with new plugs

Relates to Link       http://fepower.net/simplemachinesforum/index.php?topic=7684.0

Paul, wanted to thank you for the input you gave me on my thoughts about EFI.  You showed where you put a pressure regulator and a routed your fuel supply and return up the passenger frame rail
Got me to thinkin, what does a EFI have that I don’t have which would help with my Vapor Lock problem and the main thing I could see was the fuel return line, and following your idea of running it up the fire wall rather than the usual in front of the engine.  Guys still tell me that EFI is still the way to go, but I decided to just put a return and use the Holley 65# Pump and filters and a regulator (with a return) to drop back down to 5# before I go and invest in a throttle body.  Well I had the ole girl out in 90+ weather in some traffic an never a hint of vapor lock even with my hood shut, so my confidence is up.  If I ever decide to go EFI I just need to pull the regulator and plumb directly.
 Thanks everyone who passed on their experience and ideas…….Bill

The ledge at the bottom should stop the plug from shifting as you set it. 
Looking at your pic; you can see that you are already into the main center galley, so that ain't working and I'm not about to advice you to go to 3/8 npt because you could never back up to the welch cup.
Oh and the relief valve in the back.  That seems to be a size that Ford invented so don't try to tap with anything standard just clean it good with a rifle wire brush and use the kit from 'Precision Oil Pumps' and you should be ok. 
 I just rebuilt my '406' a couple of years ago so it's not like I don't understand your frustrations.

Bill

Doug, You're not missing anything.  I was a machinist for too many years with people telling me "all you got to do is", till I start showing them the things they don't see.  You ought to try explaining to people about up dating a 62 block for a cam plate.  Anyway to tell you the truth the only hole I felt comfortable with tapping was the front of the center main because the Tangent point for the feed hole from the filter was so far into the block, as your pic shows.
Like I said those plugs do work, been working on my '406' for years.
My advice, put those drills and taps away and bag your new plugs and #2 permatex till your block is good and clean and ready to assemble.

Oh and guys its a center oiler 427 solid lifter block so there is no hole behind the distributor to tap or plug.

I use Remflex gaskets, they work great but are fragile. I would recommend the use of 1” long header bolts with the use of the thicker flanges of today’s headers, would rather see the bolt peeking out the back then not using all the available threads, especially if you use aluminum heads.  Some flanges have slotted bolt holes to make it easier to hang your headers so there I use a flat washer and of course a high temp never seize such as Jet lube 550 on all the bolts.  They have these special header bolt 'Stage 8'  but they look to be more trouble than they are worth, but maybe worth a look.