Welcome to CHR, Harout! Sounds like you want to build a traditional kustom. Some parts for 54 Chevy's are available both in nos and repro while others may be difficult to come by. Should be plenty of room in the bay for a sbc, even a bbc. Make sure your body is as rust free as possible. Good solid sheet metal is desired. Watch for excessive bondo or poorly performed repairs. Having good bumpers (good chrome, little or no damage) is desirable as new ones could run you several thousand dollars. Suspension should be an issue since you are likely to replace nearly all original suspension parts and the brakes.

As for chopping the roof, I can't directly address that, but others here may. I have a friend with a chopped 53 and his is excellent. How much time and money, I don't know.