I build a bunch of strokers, Windsor, FE and 385 series. All are good.
A Windsor, 351 or 302 based, makes a lot of power on the cheap (relatively). Lighter, easier to find parts, and makes for a really strong combo. Last 347 I did made 490 HP with a 216 duration cam, and 13 inches of vacuum...hard to beat for something driving often
A 385 is heavy, but the power that can be made is incredible. Cheaper than an FE for the most part, but IMHO not quite as pretty under the hood of a Cobra. Although brutal torque on a nose heavy car is really lopsided in my view
The FE is unique, but correct for a 427 car, they run great, we can click off a Sunday family driver, no maintance at 550-600 HP and 600 ft lbs in our sleep, and as an example, my own 489 has been together since 2006 and behaves like a new engine. In fact, I have a 505 in the works but can't find a reason to take apart the 489
If you were to come into my shop, I'd look at budget, use, which Cobra kit, the owner's personality. I'd personally push toward an FE if a 427 car, but if someone was on a budget or just wanted the looks of the car, the Windsors are a very nice combo
FYI - Even a stock stroke 390 can be brutal in these cars and brings the budget way down.