I desoldered all the QSBs. Since I only have one pin header (I lost the other :/), I pulled out individual pins out of the pin header and soldered the pins to the mobo and used the pin header cable to read to nand. I read the nand twice and compared and had 0 non-matching blocks

(I will post pictures later as I am busy atm).
So it must have been my soldering like Martin C was saying. Therefore I will resolder and replace all the parts in the jtag/smc part. Will these 1N4148 diodes work for this?:
http://www.maplin.co.uk/signal-diodes-19076?ordercode=QL80B
If this doesn't work would you recommend wiring 3 330ohm resistors instead? Thanks.