No modifications needed for the two off the shelf flywheels available, other than cutting a notch in the bellhousing for the sensor. Both are ready for the OEM EFI off the shelf.
So you have to buy a flywheel anyway? And balance it for a Magnum? Why not just buy one from MagnumMopar? You could even get it with the notches cut in it.
Don't see how your plan is any better by going to a TBI setup.
I agree that the beer barrel intake is a limitation, but I suspect it isn't that far off the mark for what you are talking about (300-325 hp). I'd bolt it on and go with it for now.
Later on if you wanted more, then buy the Hughes one to replace it.
Pretty sure Hughes and Indy are the only places selling an EFI Magnum intake anymore. Mopar Performance discontinued the two they sold and I don't believe Edelbrock sells an intake with injector ports cast in. Not a fan of the Indy intake, unless I was going to supercharge the motor. Not an ideal intake out there, but at least there is still a source for one (for now).