The reason for the supposed "incompatibility" is because there are 2 lengths for Modular pumps. '91-'01 engines all used a "long" pump, however in mid-'01 they began phasing in a newer "short" pump. More than likely the short pumps came to exist because of a change elsewhere in the Modular world of vehicles, didn't the Mustang get a mid-gen refresh in '01? Either way, from then on, the cars all got the short pump. Most trucks retained the long pump because they kept their mechanical fans and the longer pump housing offers more support for the extra weight hanging off of it.

I want to say the '01ish Cobras with the DOHC used a short length pump with the updated impeller design. That was the origin of that design of impeller. The DOHC Navigator and all 3v trucks used that same impeller design, but they were the longer pump because they used mechanical fans. I would imagine a 3v Mustang does too, and would just use the same "short" pump as the earlier DOHC. So for me and my '98, I used the Navigator/3v pump. So what if I have threads on it for a fan clutch I won't have? For you and your '06, you would need the cobra DOHC pump. However, I believe at some point all of the Modular engines had the updated impeller, so it might not even matter as it might be what your car already has.

All of this ultimately doesn't really matter because the pumps actually interchange completely. The only thing you need to change is the pulley so the belt stays aligned. So if you get the "long" pump, you need the "domed" pulley that goes with that pump type. If you get a "short" pump, you need the "dished" pulley that goes with that pump. Or just get a pump that works with the pulley you have. All Modular V8's and even the V10 all used the same pump mounting flange so it doesn't matter if its a 2v/3v/4v, the pumps physically fit the same on the block.

FWIW, here's my '98s original pump next to the upgraded/updated pump (from a 3v F150):


You can see the huge difference in impeller design. I didn't do it as a pre-planned upgrade, it was because I needed a new pump and decided to get the better one while I'm at it. I didn't have any overheating issues before, and I still don't after, can't say I really noticed a difference other than it not seeping antifreeze. I would expect its pretty much the same reason you would do it.

I actually pulled that water pump info from CVN.

The FRPP pump was either from ADTR or AM. IDR it was a long time ago. https://www.americanmuscle.com/ford-racing-oil-pump.html $81.99 + free shipping right now, you'll need to notch the oil pan baffle

Is that where the head meets the block?