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This is just my opinion, but if you wanted to stick strictly to 351ci of displacement, then the windsor is the way to go. The aftermarket is enormous for the windsor as pretty much everything for the 5.0L will work with the exception of brackets, intake, blah, blah blah.
The 351M on the other hand, is merely a 400 with stunted growth issues. They made the 400 first, and then destroked it for the 351M to be used in more cars. As we all know, the 400 in stock form wasn't anything to get excited about, and by extension the 351M is basically a lesser version of that.
Mind you, my arguments are keeping to the point that you're sticking to the same displacement. If you were looking to go bigger, then my arguments would change considerably. The 351W can be stroked, which I think typically goes to 392 with a scat crank, but I've seen bigger windsors.....as for their longevity being that big, I doubt they'd last forever. The 351M on the other hand, basically being a 400 already, but with the wrong crank....opens the door to not only bring the 351M back up to 400ci, but also to stroke it to 434 safely. There are guys that have stroked that plant well beyond that, but again, longevity plays into the equation at some point.
As for simple apples to apples sorts of comparisons regarding the windsor versus the modified, that probably gets into a matter of taste.....some guys love the windsors like I do, but some swear by the modified as well (whereas I'd just make it a 434 and be done with it). I can say that the windsor doesn't have the reputation for low compression, retarded timing, bad oil pressure that the modified does, but every issue the modified has can be addressed if built right.
I guess the simplest answers would have to come from what the intent would be of the motor.....car use, truck use, big displacement, stock displacement, big power, high rpm power or low rpm power, etc, etc, etc, etc. Once you determine the specific purpose of the plant needed, the utility of each engine will become more clear.
351m is a good motor but a 351w is a better block to chrome out and show finish up. However while there are more parts for a windsor will you ever actually buy them and use them? Its a serious question, dont buy a block simply because someday you might want to put accessories on it/in it.
Id pick a windsor because id want to have a supercharged v8 in a truck for the stupid reason of simply having it. my Modified block makes this desire less likely to happen. However my modified block has never given me any problems and it sure puts up with all the stupid abuse i put it through.
Windsor all the way. Whether that's with stock displacement, or stroked. The stock 351w doesn't suffer the same common problems as the M, but as Behemoth mentioned all these can be fixed if you are building an engine. That said, if you are building an engine, I would lean even more towards the Windsor. It's cheaper and has better parts support. They are commonly stroked to 393, 408, 418, and 427ci. A stroked M does have a cool factor of not being done very often, but that's also why it's more $$.
I like the M becouse you just have to bolt on a crank, and you'll have 400. Spend a couple more bucks, and it can be off-set ground to like 420ci.
The above provides your going with either Aussie 3V's or Edelbrock heads with matching intakes.
If you wanna just build a good motor to drive around town I would go with 351W, becouse the heads are better for todays gas. Rather the 351M's open chamber heads vs the 351W's D-chamber. Or if you upgrade to cheap late model 5.0 heads which are a great option for the money.
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