That's the better route...that way you can still have fun and have a trans to back it up...you'd end up needing a trans anyway with a 426 too, well I would go with one...along with all the proper head parts, cam, fluids, might as well get headers while its taken apart...labor, tuning.
Like Skip said, you'll need a tranny either way. The blower power will wear on it, and a stroker's torque will wear on it.
426, heads & parts, cam, torque converter would be a good idea to really bring things together, headers will help a 426 exhale, plugs, injectors and tune. Ported intake manifold would be great, matching 90mm throttle body, too!
Blower, injectors will come with it, but if you plan on more boost you might need to get new ones, then plugs, a solid blower cam would solidify things, ported heads would help with air flow, torque converter wouldn't hurt, and tune.
So many ways to blow your money! And it's so easy to keep adding things to the list as you go!!!
Transmission would really lock things up either way you go. Installation varies depending on your surrounding shops. Here in Phoenix you can have a blower installed for $500 at one shop, or $1,500 at another. Removal and installation of engine could vary from $1,000 to $2,500, not to mention the other labor of piecing the 426 together.
If your going with a 426 stroker with all the parts ,(cam,heads, ported intake ) and so forth which to be honest you need to other wise just upgrade your 6.1 and a new trans you will be around the 20G if not more. Depending on who you get to build it for you. Remember doing the job right with quality parts and set up right the first time is the way to go. IMO you don't just look for who is giving best deals or group buys. No matter what anyone says in the end you get what you pay for, no truer statement.
First thing to do is figure out what you really want. Will you be really going to the track? Is this for street us also, or a real daily driver? What is your end goals? Don't get caught up in the let everyone spend your money trap.
Remember no build can say for sure what HP you will have, as well as HP does not equal faster times. Also work with your builder, plan out each step as well as get everything in writing. This should include a time line, clear explained in writing warranty especially if your having set up installed by someone else. Get a list of all approved tuners that your build will work with. There really is a difference in different companies builds best advice that anyone should tell you is do your research, not just on this forum but every where. Look into how many builds had to be corrected just to get daily reliability. Make sure you talk to any builder to go over street zones and inspection passing, get it in writing.
And most of all after my long somber post lol have fun, don't rush it, and it's better to wait just a little longer if you have to save to get it done right up front. It's a long expensive tail chase trying to fix due to some skimping.