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Re the image of the three lifters, they are all different lengths when they should all be the same length. Of course you could compensate for these differences with adjustable rockers but that would be a kludge that will inevitably cause problems. Clearly, you will need a new set of lifters with the stock rocker arm assy..
Re pushrods, stock pushrods should work with the stock rocker arm assy you ordered UNLESS the deck hight of the block (decking) and/or the height of the cylinder heads (truing/resurfacing) was reduced significantly by machining. At one time Ford actually offered pushrods that were 0.001" longer to address this situation. Advise that you obtain a pushrod measuring tool. Oil and prime all the lifters first and then measure (with an appropriately sized caliper) all 16 pushrod locations. They should all be the same give or take a few thousandths so you can derive the average and compare that with published stock length.
All of the above assumes a stock cam and stock valve springs.
I sent that picture of the different length lifters to the builder and he said "you didn't break in the engine properly." Can anyone tell me if that makes sense. Could those lifters be different lengths because of something I did?
Wiping a cam lobe isn't a rare event on break in but I cannot imagine you ground that much off a lifter. what does the bottom look like ? normally the cam takes the worst of it and the bottom of the lifter is messes up some. there is no way a cam survives grinding a lifter down.
The pictures look as if the cups on the push rod is contacting the rocker arm. this is unacceptable, unless your new lifters are shorter you're going to need shorter push rods so the adjusters can be moved out of the hole they're in. god only knows what your geometry looks like.
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