First, I'll talk about my thoughts and then give you some facts below
If you want to have block security, assuming you are wanting to drive a 400rwhp stroker as a daily driver, I would suggest upgrading a B50 Sportsman block (guys have gone in the high 120-low 130 mph marks with that block) or a Dart Block which is much stronger even than the B50. The B50 block is $1000 and the Dart is $1900.
Remember there is a difference between a daily driven car and a street car.
They can be made reliable if you have a good builder

This is further explained below.
I have a couple friends with 347 cubic inches and a couple with 331 cubic inches. Both are nice in their own ways
A few days ago over on the corral, there was a racer that couldn't get his 347 with a 5.400" rod to prevent blow-by. He had it at a couple reputable shops to rebuild it. Oil ring problem or other? I'll let you decide...
Stroker Info
http://www.strokerengine.com/RodStroke.html
http://www.fordmuscle.com/archives/2003/09/stroker/
http://www.mustangandfords.com/techarticles/5197_331ci_stroker_engine/
Piston diagrams:
http://www.ariaspistons.com/pistondiagram.html
The 3.25" stroke (331) and 3.4" stroke (347) both make similar power numbers.
The 3.4" (347) stroke DOES have a steeper rod ratio.
A stock 5.0L displacement is 302 cubic inches. It consists of a 3.00” stroke and 4.00” bore. The stock rod is 5.090”.
A 306 is created by reusing the stock 3.0” stroke but boring/honing the cylinder walls .030” to create a 4.030” bore. It utilizes an oversized piston, larger than the stock 4.00” stock bore/piston. A 306 is a form of a budget build and is not intended to make extra power, but to create fresh cylinder walls for longer engine life and revive lost compression through high mileage engines.
Both the 302 and 306 reuse stock 3.00” stroke crank and stock 5.090” rods. The 306 needs new oversized pistons.
A 331 cubic inch engine (stroked 302), consists of a new crank of 3.25” of throw, and the 4.030” overbore that creates fresh cylinder walls. To get the 331, you need a crank, of 3.25”, new rods of 5.315” or 5.4” length, and a .030” overbore from stock bore.
A 347 consists of a 3.4” stroke, 5.315” or 5.4” rod, and oversized pistons of 4.030”.
The vast majority of 347s and an occassional 331 need extra cylinder skirt block clearance at the cylinder walls to clear the rod bolts as a crank rotation is being made. The throw of the crank is too large to have safe tolerances to rotate.
Piston speed in feet per minute:
A 302 with the 3.00” stroke moves 3,000 feet per minute.
A 331 with the 3.25” stroke moves 3,250 feet per minute.
A 347 with the 3.40” stroke moves 3,400 feet per minute.
Faster piston speed equals faster wear and the need for a bit stronger components as the fpm increase.
Excellent Unbiased Information Below:
http://www.fordmuscle.com/archives/2003/09/stroker/
If you want to read about how steep rod ratios affect performance...read this:
http://www.strokerengine.com/RodStroke.html
If you are going to build a true street car (daily driver), get the 5.315" rod. The only real advantage the 5.4" rod has is it's longer dwelling time (very slightly different which is irrelevant) at BDC/TDC which gives those drag racer/track kings that very slight edge over the next guy.
The offset wrist pin the 5.315" rod makes that rod act like a 5.415" rod anyways (.100 difference) without the oil ring/wrist pin intersection.
Mark O' Neal at CHP/Probe recommends it for street engines.
Daily Driver = 5.315" rod – 1.175” Compression Height
Track Car = 5.4" rod –1.090” Compression Height
5.400" Rod 347 vs. 5.315" Rod 347
Left is a piston with the wrist pin intersecting the oil ring land; 5.4" rod piston.
Right is a piston where the wrist pin does not intersect the oil ring land; 5.315" rod piston.
The additional leverage applied to the cylinder wall (thrust) side of the shorter 1.090 compression height piston combo makes it even more important to properly bore, hone, and ring gaps to ensure any type of longevity. The longer 1.175 compression height piston combo is more forgiving by allowing more room for error, because of the longer skirt and pin location. It also provides better oil control.
The use of a good dimpled oil support rail (needed for 1.090" pistons) that can't rotate in the groove (due to the dimple facing down into the pin bore and effectively locking it in place), you can help combat "extra" problems with oil consumption. Bad ones, use what amounts to a 3rd oil ring wiper with no dimple that clamps against the back of the oil ring groove and they can rotate and/or roll in place. A good builder and parts used are key. Here is a picture of an oil ring support in an aftermarket ls1 stroker piston, which helps put text to visualization:
http://www.gmhightechperformance.com/tech/0608htp_ls1_engine_build/photo_58.html
The oil ring support goes underneath the oil control expander on the very bottom, if looking at the piston from it's 'in engine' orientation. The oil support rings go directly above and below the oil control expander, with the oil ring support on the furthest wrist pin side.
The 5.4” rod piston has a shorter skirt, which causes it to be a bit more unstable from top to bottom.
5.4” (1.090” piston) combo is sometimes considered lighter than a shorter rod – 5.315” rod with 1.175” CH.
Probe’s lightweight 4340’s are 510 grams for the 5.090” rod, 520 grams for the 5.315” rod, and 530 grams for the 5.4” rod.
The ultra light 4340’s are 531 grams for the 5.4” rod, 530 grams for the 5.315” rod, and 518 grams for the 5.090” rod.
The 5.4” rod and 4.030” with the 3.4” stroke’s piston weighs 474 grams.
The 5.315” rod and 4.030” with the 3.4” stroke’s piston weighs 474 grams.
Using this example, the piston/rod combo, whether using a 5.315” rod or a 5.4” rod, the rotating weight is virtually the same. If not the lighter side, going to the 5.315” rod in this example.
The weights are approximate and could very well go the other way.
If long engine life and reliability are your goal (daily driver), keep the piston pin out of the ring area, by utilizing the 5.315” rod and 1.175” compression height piston. Having the piston pin close to the hot piston crown is just asking for premature engine blow-by or even failure. The oil struggles to stay on the wrist pin/boss because heat chases it away. The taller compression height also directly strengthens the piston crown.
It is a very easy concept.
So in short, to get the cubes and best reliability from those cubes possible, you can go 331 (5.315” or 5.4” rod) or 347 (5.315" rod, NOT 5.4” rod). Get the cubes and mileage you are looking for = 5.315" rod for the 347.
Remember it is your money that you are spending.
Good Luck!
Now, as far as nitrous or supercharged applications, the 5.315" rod in the 347 appears to be better as well. The top piston ring may live a bit longer as well.
Here is some info posted by FastDriver about picking a 3.25 inch stroke over a 3.4" stroke:
I forgot to mention the biggest reason CP didn't like the 3.4" stroke. The ringlands on high boost application pistons has to be lower, which runs you into a bind if the pin is already intersecting the oil-ringland.
There are three reasons as I understand them:
1. The easy explanation is that the higher you place the rings, the more heat that they are exposed to making more prone to fail - there is a thermal barrier between rings that are lower on the piston and the combustion chamber that is created by less efficient burning of the gasses between the crown of the piston and the cylinder wall 2. The thinnest part of matrial at the crown of the piston is the "meat" between the top of the piston and the 1st ringland making this the most likely part of a piston to fail in many applications, and 3. the higher the ring the more prone it is to fail due to mild detonation. As you can see from the article I quoted below, this is not optimal for a naturally aspirated engine:
The "dead space volume" above the piston up to the top of the cylinder wall usually traps unburnt fuel and burns less completely...producing more emissions. Reducing this volume, by moving the top ring up , decreases emissions. The top ring is now exposed to hotter temperatures and must be stronger.
However, moving the top ring up is not just for emissions purposes either:
Here you see a higher top ring and piston pin location placed at the level of the oil ring groove, both of which allows for a longer rod and better rod ratio in these forged race-only strutted pistons.
Moving the top ring down improves durability but at the same time, creates a situation where more entrapment of unburned gases will occur locally in that area, leading to a less efficient burn.
If you want more technical information concerning the subject talk to a tech named Mike at CP. He once explained the subject to me and at the time, I felt I had a very good understanding and I was in agreement with his assessment that I should go with the 3.25" crank instead of the 3.34, 3.4, and 3.5" billet cranks I could get at the time.