FE's in general or specific FE's in particular? 352's are unlikely to increase in value in this lifetime or the next! 427's will, but it's complicated and there is no easy "yes" or "no" answer to the question.
Top oilers are not going to carry there value as well as side oilers, thats a fact. Among side oilers, DATE CODED 1965-66 blocks will carry more value than say a later model service block. A NOS block will carry more value than a sleeved block, repaired block vs stock, etc.
Some specific FE blocks are certainly being horded by engine builders. THEY expect to turn a nice profit on these engines building them for customers who want a period correct FE. And are willing to pay for it! The professional builder has the contacts, reputation and authority to market the engines with some success. It is unlikely you or I share these same traits.
The real value of a side oiler is when it comes with the CAR! I think you would have a tough time trying to sell the engine by itself and get a reasonable price. Let alone a 'profit'. But just try to BUY one, just try! There hard to find and will cost you a bunch!
You can bet on one thing. Ford didn't redesign the top oiler into a side oiler just for 'bragging rights'. They are far more intelligent than that.
