it's weird that it started when you replaced the intake, then discovered the intake had issues and fixed that, yet it continues.
can you replace all the parts without gaskets and determine if the angle or clearance between parts is acceptable?
if everything looks good here and things are installed properly you will have to look elsewhere.
next time you get everything together, and i guess you have changed the
oil a couple times, and after eliminating all other possibilities, i would put some pressure into the cooling system with coolant installed of course, and if you can drop the
oil pan i would look at the bottom of the cylinders where the liners meet the block and see if there are any leaks.
just a thought, don't know if this is a possibility, or maybe you will be able to see if there is a leak coming from somewhere else, or at a minumum you will be able to tell if it is holding. of course if this is happening only when hot, that complicates things, but aluminum does expand quite a bit more then the steel liners.