Money is an issue. You will be selling the Ducati for sure and you don't want to do that. If I sold my FJR I know I would not have a another for a long time and I would miss it. FE's are expensive to do it right. Stay with the 302 block and go 331 stroked. Ask the builder to give you a price on rebuilding your current heads, if they cost more than $1000 to rebuild then go with the Edlebrock or maybe a set of World or AFR heads. Install 3.25 or 3.31 gears in the rearend and you should be good to go. All the other parts should fit up in the rebuild.
On the Cooling issue: Check the radiator out while you are building the motor. Install a electric fan if you don't have one and run a
oil cooler. Might be able to get in under 5000.00