Let me try to answer your questions in order.. I have built several of these engines both stock and performance.
Intake manifolds are a problem The only single 4bbl holley pattern intake is cast iron and is found on the 332 heavy truck engine from 1957 to 1964. They occasionally show up on ebay.
For Aluminum, there are only multi carb intakes . The factory M-335 intake used on 57 Mercurys is the best of the lot but rare and expensive. Edmunds made a 2x4 and a 2x2 intake but these are also scarce..
For my performance Lincoln Y blocks i use an aluminum spacer, and adapt a small block scruby intake
Ford Y bock header will not fit.. There are header flanges available, and what I do is adapt header from a small block scruby, or make my own.
A Ford Y block distributor will fit the Lincoln if you change the drive gear. .MSD has them, or you can convert a stock 57 and later distributor to electronic
Bearings and other engine parts are availbale from several Vendors Check Ebay
My friend Rick Martin has run the Pan america race in his 53 Lincoln.. You might contact him for advice.
martinrp2@aol.com.....I believe he even has some video of him running flat out down a long strait stretch of road...
Your Lincoln engine is very rugged and will hold up well to just about any amount of reasonable horsepower you throw at it.. My 57 368 based engine has made hundreds of dyno pulls survived 3 engine masters competitions and made dozens of 1/4 mile runs in my drag car.. it makes 520 horse and 500 fit lb of torque and pulls to 6500 rpm..I have never even had the oil pan off of it during this time.
I will be happy to give tech assistance or help track down parts for your car,,Royce Brechler