You need a MC specifically for 4 wheel disk brakes. The 1988 MC is still spec for rear drums, so if you install it your pedal will be extremely soft, and the travel long. You'll be rather disappointed in your braking performance
Assuming you used rear SN95 disks, the MC you should use depends on which Cobra calipers you installed.
94-98 with 38mm pistons = 94-95 Cobra 15/16" bore MC
99-04 Cobra/bullitt/Mach1 with 40mm pistons = 1993 Cobra 1" bore MC.
Best way to tell the difference between the Cobra calipers is to look at the underside of the piston bores. The 94-98 38mm calipers have ribbing on the bores, while the 99-04 versions are smooth.
38mm on left, 40mm on right
Once you've identified which front calipers you need, you just need the MC and adapter kit. I've usually sourced my MC's from parts stores as they tend to be cheaper.
MMBAK-9 is the adapter kit for 94-95 Cobra 15/16" MC
http://www.maximummotorsports.com/M...master-cylinder-in-1980-86-Mustang-P1273.aspx
MMBAK-17 is the adapter for the 1993 Cobra 1" bore MC
http://www.maximummotorsports.com/M...master-cylinder-in-1980-86-Mustang-P1273.aspx
Another option if you determine the 1" MC is what you need, is a 1985 Lincoln Town car MC. It matches the style of MC you currently have, and may be much cheaper. Downside is you need one adapter fitting where I don't have a source for. Refer to this chart
http://1985mustanggt.com/Reference/2009-09-19_Mustang_MC_Info.pdf
Thanks for the reply!! What about the booster?
As for the prop valve, gut the stocker by removing the front nut and install the prop valve plug part. Then, install an adjustable unit on the firewall at the pass side rear firewall union.