You may want to review the IFIXIT guide here: [guide|11713|Installing Mac Mini Late 2012 Dual Hard Drive Kit].
Are you sure you disengaged the DC-In cable from the logic board as outlined in Step16?
Sliding the logic board out can be tricky! It does not take brute force! If you have already forced it you may have damaged things. The first 1/8th of an inch out can be tight as the grounding clips tend to grab the shell a bit.