I got a disc/drum master cyl on my shelf but it's for power brakes,I need manual can I drill the piston deeper for the push rod?
That really doesn't sound like a good idea. The single most important thing on any car are the brakes. I would "bite the bullet" and get the proper master cylinder for the application that you are in need of. Better safe! KK
Using a master cylinder with a deep counter bore on a custom manual system is good practice, especially if the push rod will not be retained in the bore, like most/all factory manual push rods. However, do not attempt to drill a shallow bore primary piston, because manual and power primary pistons are usually designed and configured differently. You may drill through and/or weaken the piston. JFYI, all of the Ford power brake masters I have, use or remember working with have the deeper push rod counter bore, normally around 1 1/4" or so. The manual masters I am familiar with have the push rod retained in a shallow counter bore.
Master cylinders are so inexpensive these days that it's not a place to scrimp, considering what the outcome might be.