Hello,
I am having a issue with getting some electrical back in order, I took down a wall that was in the garage and pulled and labeled all the wires. I have rewired and put back all but one section of the wiring which seems to be giving me a problem, 

The wiring that was pulled back went like this…

junction box 1
(All whites together, all blacks together, all grounds together

down to light switch (two separate single switches)

first light switch on the left top screw  black wire coming from yellow left bottom screw black pig tail

second light switch on right top screw black wire coming from yellow right bottom screw black pig tail

yellow wire, white wire, yellow wire coming into box 

the remaining blacks was bunched same with white and grounds 

that was required and works as it should 

wires continued down to another junction box a gfci and a light switch 

two yellow wires 
two white wires 

junction box comes first then down to gfci the up to light switch (3 way) 

GFCI
left.               
black coming from left white wire 
black coming from right white wire

right.
white coming from white left wire
white coming from white right wire

grounds together

light switch (3way)

top left screw red from white right wire
top right screw black from white right wire
bottoms right screw black pig tail

from the second junction box there is another wire that continues down to some lights 

the problem I am having is with the 3 way and gfci I got 4 wires coming in two yellow two white 

(white left, yellow left and white right which has a red wire in it, yellow right

yellow left is hot the other lines have no power coming to them

can anyone help me figure out how to wire this gfci and switch (3way) they was in separate boxes but I took out two extra wires one white and one yellow which was there when wired in the beginning but was able to take them out when I moved them to one box. 

(Picture included was how it was wired to begin with light switch in front, gfci behind that)