Eastern,
You can order any year Ford Colone 2.8L pistons, they are all the same (* correction, I believe that there are some 2.8 pistons that use an undesired compression height, but I can assist with that
), all flat top; just be sure to get the correct bore or over bore. The reason to use the 2.8 flat tops is they will increase the compression ratio approximately 1 full point over the stock dished pistons.
There are no clearencing issues using the 2.8L flat tops (bar the compression height, as mentioned above) just the improved performance firm the increased compression ratio. There are several reasons to consider milling your heads 0.03", the primary is having true flat Matting surfaced to work with but this can usually be achieved with much less material being removed. The benefit of removing 0.03 of an inch is it will also increase the compression ratio.
I did exactly this with my 1st 2.9L build. My machinist suggested 0.03" shave with those piston to result in approximately a 13:1 compression ratio from the stock 9:1 that is a useful performance increase. My rule of thumb formula for compression change is 4hp/complete compression ratio point increase; so that's +16 ponies with torque benifits too.
Adding 16hp to a stock 140hp engine in a pretty serious improvement. If you go the step further and have your heads and intakes flow bench port/polish you stand another gain another solid +20hp. The customer ground cam, +20hp and complementing it all with a good set of headers is +20hp more. All of these efficiency improvements mean that you will experience maximum fuel economy with quite a bit more SNOT ..)