If conditions in a Makefile, inside a target

There are several problems here, so I'll start with my usual high-level advice: Start small and simple, add complexity a little at a time, test at every step, and never add to code that doesn't work. (I really ought to have that hotkeyed.)

You're mixing Make syntax and shell syntax in a way that is just dizzying. You should never let it get this big without testing. Let's start from the outside and work inward.

UNAME := $(shell uname -m)

all:
    $(info Checking if custom header is needed)
    ifeq ($(UNAME), x86_64)
    ... do some things to build unistd_32.h
    endif

    @make -C $(KDIR) M=$(PWD) modules

So you want unistd_32.h built (maybe) before you invoke the second make, you can make it a prerequisite. And since you want that only in a certain case, you can put it in a conditional:

ifeq ($(UNAME), x86_64)
all: unistd_32.h
endif

all:
    @make -C $(KDIR) M=$(PWD) modules

unistd_32.h:
    ... do some things to build unistd_32.h

Now for building unistd_32.h:

F1_EXISTS=$(shell [ -e /usr/include/asm/unistd_32.h ] && echo 1 || echo 0 )
ifeq ($(F1_EXISTS), 1)
    $(info Copying custom header)
    $(shell sed -e 's/__NR_/__NR32_/g' /usr/include/asm/unistd_32.h > unistd_32.h)
else    
    F2_EXISTS=$(shell [[ -e /usr/include/asm-i386/unistd.h ]] && echo 1 || echo 0 )
    ifeq ($(F2_EXISTS), 1)
        $(info Copying custom header)
        $(shell sed -e 's/__NR_/__NR32_/g' /usr/include/asm-i386/unistd.h > unistd_32.h)
    else
        $(error asm/unistd_32.h and asm-386/unistd.h does not exist)
    endif
endif

You are trying to build unistd.h from unistd_32.h; the only trick is that unistd_32.h could be in either of two places. The simplest way to clean this up is to use a vpath directive:

vpath unistd.h /usr/include/asm /usr/include/asm-i386

unistd_32.h: unistd.h
    sed -e 's/__NR_/__NR32_/g' $< > $@

You can simply use shell commands. If you want to suppress echoing the output, use the "@" sign. For example:

clean:
    @if [ "test" = "test" ]; then\
        echo "Hello world";\
    fi

Note that the closing ; and \ at each line are necessary

(This is because make interpret each line as a seperate command unless it ends with \)