They do not make after market rod bolts for the 3.0 rods, I checked with ARP when building this motor I am running now, 2 sets of custom made rod bolts from ARP was $800 - 900, as they are true one off specials, and there was nothing they already built close enough to allow machining of stock rods to accept a stronger bolt. Rods seem decent as for strength, nothing bent in the other motor & it let go at 5500-5600 rpm, by the time I got it shut off it had broke 3 more rods from the shrapnel but they broke near the big end. As for porting, The set of heads I have on here now are huge for a 3.0 & highly polished, I did loose some low end torque, but thats not a big deal when you can set it sideways at 25mph anyway, and what I gained on mid & top end more than make up for the torque loss. So just be careful on your porting, especially if your not going to run 10 psi or more. Porting to exactly match the headers is a bad idea, you need your exhaust ports approximately .035 - .060 smaller diameter in the head than in the header to avoid reversion pulse. We always have that little step, it helps to increase velocity at the exit & it tends to center the flow path towards the center of the header tube, same goes for the upper intake to lower & lower into the heads. As far as the pistons, the stock ford 3.0 slugs seem to have a good thick top section, and a fairly low top ring position, that's what you want for boost or nitrous, They could be al little lighter, just be careful to control the cylinder temps & you should be fine, even with them being cast. I would not put dished pistons in on a street motor, the lower compression will make it a dog anytime your not into boost, I like to run high compression & then control the detonation. An all out race motor is different animal all together. Mine saw 22 psi for a while on the motor that blew, all the pistons looked brand new even after it let go.
As for running out of meth during a wide open run thats not a problem either as the Explorer has a really nice warning light setup on the windshield washer fluid, even with the light on you still have enough for 2 full passes on my nozzles.
If I was going to go the M90 or M112 I would choose the 112 as you could easily adjust the pulley size to lower the boost or run a BOV / bypass & this would help lower your intake temps after the SC, if you go the other way with the 90 & have to spin it harder than stock (smaller pulley) its going to make a ton of heat as you increase the boost. These chargers are well know for that, the Cobra / Lightning crowd likes to dump them for the Whipple, which is a more efficient compressor style. And as was mentioned, as far as porting, valve jobs etc the better job you have the less pressure (boost) will be on the motor & your still making more power due to the increased airflow. As for the MAF, a 4.0 works very well, although I did not have a lot of room left in mine at the 22 psi mark. & if you plan on running E85 plan on tuning for injectors that are approx. 30% larger than if you were running gasoline as that is about the ball park difference in the gas - alcohol, sometimes large injectors can be difficult to tune to idle smoothly.
I personally would like to have one of Tom's stroker motors and add 22-24 psi to it, I bet that thing would just be a little monster.
JP02XLT