I assume you are trying to fit a 4.3 Vortec, not a 4.2. Is that correct?
The exhaust manifolds used on the 4.3 were different (one piece) than the 2 piece ones you had on the 3.8. They are the issue you have with fitment and will have to be changed to the one piece style in order for them to clear the intermediate housing and tilt motor.
The issue you will run into is that these manifolds are no longer available. you should try to source them from a dealer who has a stock pile of used OMC parts.
An older, established dealer would be your best bet. Or give E-Bay a try.
Best of luck.
Marine Mechanic
Evinrude Master Technician with 27 years of experience.
Try these guys. I've never dealt with them but they do show as having the manifolds you need.
http://www.manifoldwarehouse.com/mes/mgr?brch=home
I would call them directly as you will also require the elbows and adapters for fitment to the older style exhaust housing you have.
Good luck!