I am going to be putting my engine back together and I can not decide if I should put the flat top pistons I have back into it and buy a 9 inch stall torque converter or if I should buy a 408 kit and then run the torque converter I have now? It is a off shelf 2500 stall that does not feel any different than stock. Either way I have to buy a new cam. It is going to be a street driven car. I already have a good set of ported heads I will be using. If your vote is for 408 which kit eagle or scat and where is best place to buy it?
The best price I have found is cnc-motorsports (cast crank eagle)and they say that they balance in house.

Go 408. Hughes has mnay different "drop in" ( their term )stroker kits available at good prices.

Having had a 406" 360 for a street Duster, I can say the torque was well worth it. Personally I prefer Eagle over Scat, but there are probably people who'll say the opposite.
I'd also have it internally balanced, which makes it easier to swap balancers and/or converters later. For a cam I went with an Engle dual-pattern hydraulic grind: 214/224 @ .050, .470/.504 lift, 4* advanced; Demonsizzler here on the board did up my Thermoquad; I used an Eddy Performer intake, and the car had perfect right-now throttle response, 17MPG @ 70MPH, ran A/C & power brakes without any issues. Stock converter, 3.21 gear, 275/60R15 tires, about 3400 lbs. I would do it again in a heartbeat. Never ran the car at the track, but it felt much stronger than my '97 Mustang GT.
Don't bore the block 'til you mic your pistons, and thicker walls are better IMO than the last .020 of bore size. Max CR with iron heads & 91 octane is 9.0:1 unless you pull advance out of the distributor curve.

I agree, don't bore until you have the pistons in hand. I have an Eagle kit in mine with KB pistons. I run a Voodoo cam and ported iron heads. 3500 stall 4:10s in my Dakota. I love it. Could use a little more carb for the size of cam. I got my kit out of Texas for around a grand. Have the crank and rotating assembly balanced at a reputable machine shop. I have heard too many stories about poor balancing by the distributor of the parts.

I'd go for the 408 buildup. If you're into needing pistons already, that is a big chunk of the difference in a stroker kit. I did a eagle crank and H beam kit through board member Scott Brown. My only reservation might be that you need to make sure the heads flow for a stroker, or it might run out of steam earlier than you want it (even though it's makign more power), and if you are geared for a screamer motor, you might have to re-gear for a bit less RPMs or make the 408 a screamer too. Mine makes peak power in the 6500 RPM range but it's built to make lots of power up there.

Yes for sure. I have a 406 stroker magnum with the R/T plus roller cam and it feels like a warm 440. Gobs of torque, smooth idle, all good. I had it balanced as well.