It sounds like you have a fair number of blocks & heads to choose between already.
What are your driving plans for the truck? Knowing this may help you make some of the parts and money decisions. Example: if you won't be driving it very much the cyl. bore may be 'close enough' to just hone & re-ring, saving the cost of boring the block and a new set of piston$. If you'll be using it a lot that makes boring & new pistons a more reasonable expense.
The machine shop you use will want to know if you want hardened valve seats installed in the heads, for running unleaded fuel. It's a good idea but kind of pricey. If you won't be driving the truck much you can probably get by with some sort of lead additive in the fuel.
The price difference for the machine work to rebuild a 130hp 2bbl 239 and a 245hp 4bbl 312 isn't nearly as much as you'd think. As far as I'm concerned you might as well get a few more hp for your rebuild money. The different displacement blocks are effectively interchangeable. I'd at least go with the bigger/better pieces you've already got and maybe a couple OEM part upgrades (heads, 4bbl, ?) instead of worrying about finding another engine block that may not be any better than something you already have.
As a first step it could be worthwhile to pay a few bucks to a machine shop near you to look over what you have and let you know if it's within rebuild specs or too far gone.... before you go to the trouble of taking too many of the wrong parts to a rebuild shop in a neighboring state.
Have them look at the EDB block you have, with the oil pan & heads off, and any other loose blocks and pairs of heads you have. (the heads can become right & left handed over time due to corrosion in the water passages to the intake manif. and placement of the water temp sensor fitting)
You can have the freeze-plugs pulled to check the water passages around the cylinders for internal rust buildup. If that can't be cleaned out the engine will run hot. Have the parts double checked for obvious cracks too. All this will give you a better idea of which good/repairable parts you have to work with.
I'll agree it's easier to be more comfortable with a semi-local machine shop than one on the other coast. Their price may be a bit high, or about right, depending on how complete the engine is you get back. That being said, it can pay to shop around and compare what you get for your money from other places. If nothing else, as you talk with different shops you'll become more informed about what you need and what it costs.
Also ask about swapping out the broken main bearing cap and align honing, I suspect that's an ok thing to do, but since that block was already bored from 272 to 292 they may(?) say it's too far gone. Something about 'bored past the original hardened cylinder wall surface' or 'cyl. walls too thin'.
The seized block you have, what is that one? The fact that it's seized isn't really a serious issue for rebuilding unless something is trashed past the max. spec. for rebuilding. (usually cyl. bore, thrown rod, cracks or other physical damage to the block) because the rest of the parts are getting replaced or reconditioned anyway.
If you get a good enough price on the rebuilding, from a reputable place, it may cover the shipping and you'll still have saved the difference.
Here's another really good resource for you, send Tim an email. http://yblockguy.com/
He's into old Ford trucks. Ask him about engine rebuilders, hopefully he knows of some in your neck of the woods, and the bell housing you need.
Also, bell housings turn up on ebay pretty often, just make sure it fits your truck first. Having the same casting number is a good bet, but there may be similar ones that will work, ask Tim.
This link http://ford-y-block.com/cylinderheadchart.htm has the valve and combustion chamber size & compression ratios listed by casting number / year.
Depending on what they are, the heads you swapped onto the 239 may be a good option, especially if they match and don't need any work.
Yes the C0TE heads have smaller intake valves but they are 'posted' heads, and they can safely have the chamber surface milled a touch more than the '56 & earlier 'non-posted' heads. If you are staying with a 2bbl carb the smaller intake valve size isn't much of a concern. The (two?) B9TE heads you have do use larger intake valves and they are 'posted' as well. (but not the ECL's)
It's always best to have matching casting numbers on the heads you use.
If you might want to go with a 4bbl intake setup in the future you can use the B9TE's you already have (milled slightly if you want or have to), and '57 or newer exhaust manifolds. They'll flow better than earlier ones.
http://www.y-block.info/casting/exhaust.html (scroll down to the 2nd chart, 'trucks')
Cast iron can be welded but it has to be done correctly or the edges of the repair will be too brittle and fail again. I've been told that using a gas torch for the welding works well as it spreads the heat out over a larger surface, not creating an 'edge' to the repaired area. There may be other welding methods that work as well, everyone has their own opinion. If it's been used for any length of time and not broken again you may be ok, but keeping an eye out for a replacement part is a good idea too.
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