I almost passed out. Action on the Evo board!!
Anyway, coincidentally, I have a friend who did nearly this very thing to his Evo some years ago and was disappointed with the results. He ended up with a motor that was hard to start (he installed 10.5/1 pistons), and difficult to keep in tune. I don't remember all the specifics, but for the same money you're talking about you can buy a complete S&S 96" (approx. $4500) that was purpose built for that displacement and get a better total package. This is what my friend said he should have done. Or if you have the budget and want to end up with a real race horse, for approx. $7500 you can get a complete TP 107". These would be complete, Evo design motors that would just bolt right into your frame. A shop owner here did the TP conversion to his 1994 FXLR. These are just the first two prices I could find for these motors on the web, you could shop for a deal. Then you can sell your current engine or parts to help pay for the cost of the new motor.
Anyway, with a complete S&S engine, you'd get S&S cases that were purpose built for that displacement. $4840 for the HD/S&S combo (installed) or $4500 for the complete S&S 96", but you'd still have to either do the swap yourself or pay a pro. For the $340 savings I'd have to figure the benefit of getting all new S&S, 96" designed parts and could I get it installed for $340? And again, you'd be left with some good HD Evo parts that you could sell on ebay, if nothing else, to help with the cost.
Hope this helps, or at least gives you another angle on the project. Done right, you'll have a really fun bike. Good luck.