Shrinkage seems to be genetic, just like any other side effect. Some guys suffer badly, others don't. The smaller the testes are, the less testosterone you can produce. It will certainly be in your best interest to bring them back up to size, in order to get you producing your max amount of natural test. I would try going through another PCT. For the first 2 wks, I would take nolvadex at 20mg ED while taking a sub Q injection of 1000iu HCG every 3 days After about 2 wks of this, I would continue on Nolvadex for an additonal 3 wks at 20mg. Then see how you feel from there. You may want to look into d aspartic acid to run through your PCT as well as after. On it's own, it may help with your test levels, but we want to get your testes back to optimal size first. 

In the future, it would be in your best interest to use HCG through your cycles to keep from experiencing atrophy to begin with. For on cycle use, I would use a small dose, 250iu 2x wk along with a low dose of adex to control estrogen from spiking too high and possibly causing gyno problems.