Got it figured out by changing config.txt . (Lowering the speed= )
Here is my config.txt for others with 3.5 LCD.
# — end adafruit-pitft-helper Wed Jun 3 03:41:41 UTC 2015 —
arm_freq=1000
#core_freq=500
sdram_freq=483
over_voltage=6
dtparam=i2c1=on
#- added by adafruit-pitft-helper Wed Jun 17 17:26:46 CDT 2015 —
[pi1]
device_tree=bcm2708-rpi-b-plus.dtb
[pi2]
device_tree=bcm2709-rpi-2-b.dtb
[all]
dtparam=spi=on
dtparam=i2c_arm=on
dtoverlay=pitft35r,rotate=90,speed=49700000,fps=60