Maybe I can offer some ideas...
If you really have access to the machining equipment you say you do, then making these parts should be a breeze.
But I will answer your questions to the best of my ability.
The blower swap to mustang or T-bird LX 3.8's has been talked about in much depth before. For the most part the SC 3.8L is a substantial upgrade in internal components over the standard 3.8L. Even the SC block is stronger than the N/A 3.8.
However, this doesn't mean that a Supercharger won't work on a N/A 3.8. The Roots blower is a Positive displacement pump and works well at low RPM. Read : Gut busting, connecting rod breaking low end torque. Alot of guys run vortechs which are centrifugal blowers that make alot of high midrange and top end hp. They are a little bit better in the parasitic drag department but just like a turbo, have little to offer in the lower end.
I've recommended in the past that I feel a stock compression n/a 3.8 is capable of handling 6-8psi of intercooled boost without major internal modification. Our blowers have been known to make much more than that.
Gaston did a crazy 3.8L build up that consisted of the SC block and internals, with the 99+ splitport heads and intake. He rounded out the package with a vortech. That combo was a correct combo.
One of the reasons why our cars fall flat on their face after 5000rpm or so, is mainly due to the crappy exhaust and inake manifold design. The newer mustangs (like the 99+ splitports) are designed to accelerate the flow of air over a certain RPM and allow a much larger operating space for them.
SC engines use a forged steel crank and not a cast one. That is another important piece that you have to look out for. Especially since the 3.8L uses offset crank throws. Therefore the 'meat' in between rod journals is of a different diameter than the rest of the crank. SC cranks were underfinished by .010" in the rear main journal to keep a N/A crank from being accidentally installed.
Now, there is no "how to" book or anything like that for blower porting. Certainly you can increase the blower's ability to pump air to a point with some careful porting. But any of the machine shops who have discovered porting that works are not willing to share the specifics on how to, since that is their business. If you have access to a huge machine shop, I'm sure you have access to some flow testing equipment. Try grabbing a few grenaded M90's and try different amounts of porting to a few cases. Measure everything. You might come up with something that flows good air without making huge boost numbers (this is good since it will allow the eaton to pump more air with each revolution )
And of course you may just want to ditch the M90 altogether cause the autorotor (lysholm) screw charger is the way to go. If you did figure out a way to get that to work, then work on that, since there is no bolt on kit for a whipple charger.