Since I have some free time let me summarize why I think Spider-man would win.
Matt would need to hit Pete a good amount of times or several very lucky shots to even start to slow him down where if Pete hit him once at full strength he'd be toast. As for the Kingpin fight, it's another case where they make one character stronger against a stronger character than who he usually fights to make it more an even fight. If Pete can hold his own against the Hulk even for a little while he can take down the Kingpin.
Pete may not have the formal training of Matt but between his own experience, fighting style and abilities I'd have to give it to Pete for the win if he was actually going all out. His Spider sense beats Matts radar, he's faster, stronger and more agile by far, his webbing, while limited, can be used in a large variety of ways while Matt only uses his billy club. Pete usually builds stuff in cases where he knows he needs an advantage in certain fights so based on previous encounters with Matt he'd have a very good idea on what to use to try to mess with his sense.
They both have experience fighting SPBs, they both have a large amount of experience fighting through the city and it's rooftops and they both are used to watching for civilians while fighting so which would largely cancel those factors out for the fight.
Just in previous fights against other SPBs Pete has held his own against teams of them without too much trouble. His groups even have a habits of teaming up in the Sinister Six. He's fought the X-Men several times and made them look like chumps while still bouncing around and being a smartass. He usually fights his own rogues anywhere between one on one to twelve one on one. DD usually fights one on one and hordes of ninjas. Ninjas in the MU tend to follow the
Conservation of Ninjutsu.
In every fight Pete holds himself back so he doesn't kill anyone. There's been times where he's been disoriented and he's smashed through chimneys and walls by accident and if he hit a normal person like that he'd hospitalize them if not outright kill them. If he didn't hold back and even managed to tag Matt at full strength then he would probably break something of his.
All in all if it did go where they went head to head nothing held back I'd give it to Pete. It may take some time but he'd win eventually.