What is your boost gauge reading on the different setting's? Does that ported ATS housing still have a waste gate that could be partially stuck open? Where is your boost gauge installed, hot or cold side of intercooler? could the IC possibly be restricted or have cracked hoses? If you pull the chip and reinstalled the bully dog is there a difference between stock and its 75 horse setting? Just throwin this easy stuff out there, hope it helps.
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Put a Turbo on it!!!! 
'95 F-250 Powerstroke, 350,000 Miles, Mods: Phoenix chip, 140V IDM, Diamond Eye DP to 4" straight pipe, CCV mod, Amsoil synthetics throughout.
'04 F-350, XLT Lariat, Powerstroke, CC, Dually, SS exhaust, AirRaid intake and filter, Edge Evolution, PHP FICM programmer.
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