You may be able to modify a Merlin or Allison engie to run inverted so the cowling looks right. The intake would be in the wrong place (rear supercharger instead of side) unless you add extended ducting. As you just want it to look right.
I think the main modifications necessary would be the mounting points and the oil systems. (repositioned oil pump so its right side up and possible other modifications if there isn't proper lubrication for prolong peroids inverted -in many cases oil consumption seems to go up for inverted engines)
The carburetor shouldn't be a problem as those used on the V-1710 and all US Merlins (plus later British merlins) used pressure injection carburetors which operate independent of their orientation to gravity. (basicly the same type of system as single point fuel injection or Throttle Body Injection -GM terminology-)
It should be noted that RR actually did sucessful tests on an inverted Merlin but the Air Ministry turned it down.
You may also actually be ably to find a DB engine in working or restorable condition; a Jumo 211 engine may also be a possibility.
And if you're really set on getting your own 109, reproducing one (in full scale) from scratch will be quite an acheivement, extremely difficult and expensive. (you'll need the blueprins for the entire airframe as well as proper materials and tools/machines) Fabricating an engine from scratch will alo be exceptionally difficult, even with the money and resourses.
A more realistic possibility would be finding an existing 109 airframe and restoring it (probably with some modifications). There do still seem to be some such airframes in existance in moderate (well below display, often gutted) condition, that may still be structuraly sound. I believe there were some examples of this on a thread earlier in the year on abandoned aircraft.
Edit, found it:
http://www.ww2aircraft.net/forum/aviation/waiting-found-12093.html