I have an after market ECU I will be using one thing I need yet to looking to in what information will the tranny need to see?

The AW2 from either a 2.6 or a 3.0 would be the easiest 87 to 93 or so,.The later ones have a lockup converter.
An adapter plate could be used should you want the big transmission in there as well.

Are the frame mounts between the 3.0 and 2.6 that much different? Could the engine mounts be modified slightly to make it work (like widening the holes on the replaceable mounts)

I had to go back and re- read my post, I wrote it right, The 2.6 will bolt right in where the 3.0 was.
It is the later & larger engines that have a wider mount spacing.
Here is a picture of a 3.0 bolted onto the mounts that once held a 1600, they interchange. The mounts are the same from 1970 to the mid 90s.

Sweet! That's more than enough convincing I need... I could care less about MPG, I would love the extra torque for those 33 mud tires I run.

So since the 2.6 and 3.0 are ok, will the 3.5 from the 95SR bolt to the existing 3.0 mounts? or would some welding be required?

The 3.5 block is 10mm wider than the 3.0, I expect that would mean something needs to be routed out or something. The AZ guys have done that swap so they would have that answer.

Will the fuel pump from the 3.0 provide enough to feed that turbo engine?

There are a zillion fuel pumps that will bolt right in and supply all the fuel you will need. The 3.0 pump is probably adequate. You could try it and swap it later if it's too small.

The 3.0 is plenty stout enough for the turbo (the 3.0tt uses the same internals except the pistons), but the compression ratio is too high for pump gas and serious boost. Fortunately, the above noted 3000tt pistons fit right in and have a lower turbo tolerant compression ratio. They are not forged, so I would stay under 12psi, but are therefore cheaper.

The 2.6t is stout enough to outdrag a 5.0 Mustang RL to RL. Made a lot of friends that way. The 3.0 has about 150ftlbs of torque. The 2.6 is very close to that, but the 3.0 will start to pull away in 2nd gear. The 3.0 will only watch a 2.6t disappear into the distance, with that lovely turbo whee dopplering away from you. The later 3.0's made about 145hp. The 2.6 has about 109. The 2.6T has about 180-205 in stock form (the later 88-89 ecu's allowed up to 10psi of boost, and thus the 205hp). Like all Al head/Fe block motors, you have to keep them cool. Otherwise, they are very durable. I put over 100k on a 2.6t, and only killed in a moment of madness, when I turned the boost up to 20psi and did a full bore quarter mile, or at least all but the last 100' of it. The gtechpro showed 260hp. I was running probably the second worst of the fuel systems, an 85, with limited fueling, and I got lean and detonated the top of a piston into the crankcase. Probably still be running fast today but for happy pedal madness.