What RPM Will a stroker Crank hold?

Yeah that would be the deal breaker for me.

I want to build the bottom end once! and play with the top end of the motor the rest of it's life.

Good point about care/handling of the alu rods.

If that is the case then over build your engine! I always over build my motors for the intended use. Example of this is my current 340 motor for my duster. This motor is so far from stock (the only thing stock is the block and the timing chain cover) I got:
Aluminum Ross Racing pistons
Eagle forged H-Beam Rods and Eagle forged Crank (with their ESP Armor)
Stud girdle (some argue you don't need it but it's cheap insurance and I use them in every build)
Crank scraper (Teflon bladed up and down stroke)
Milodon road race oil pan
Hyd roller cam (231/239 at .050" lift 110/106 lobe), roller lifters, comp pro mag roller rockers
Ferrea stainless steel valves, inside Edelbrock closed chamber heads (60779), Edelbrock air-gap intake, aluminum m/p valve covers, SFI balancer, SFI flexplate, timing chain tensioner, double roller timing chain on billet gears, hardened intermediate shaft, msd e-curve dizzy, and total seal gapless piston rings which is all bolted to together using the strongest arp bolts that are able to bolted in (I'm sure I missed some stuff but you get the idea).
Point is, this motor is built to withstand 1000+ but is only making ~400, this way I never have to worry about the breaking the motor.