I have heard of problems with not getting oil in a 4.6l after a rebuild since there is no way to prime the system. (I have no personal experience on this, only what I have read on the net).
Pulling the valve cover off would also let you know if you are getting oil to the top end of the engine.
With the DOHC short block and the SOHC heads, what does your compression work out to? I know going the other way (SOHC block and DOHC heads) lowers your compression by about one point. (IIRC, the compression heights are different and so are the combustion chamber sizes (SOHC vs. DOHC).
97 Lincoln Mark VIII LSC (Chip'd, 3.73 T/L... so far... )
97 Ford Aspire (Slow, but getting 36 mpg (f'n Ethenol!!
84 F250 Dually w/6.9L Diesel (7.3L IDI pending)
73 Mercury Cougar Convertible w/351C 4V (Partially Restored)
69 F100 LWB w/460 Engine
76 Glastron Carlson 23' Jet Boat w/460 CJ Engine