...
I guess it doesn't look too terrible. I also tried to remove all the listed variables as well as the first principal component and here is what I got in terms of the percent variance explained and the outliers: 
To me it looks worse than with the first principal component. Final: remove the batch, center, plate row and plate column from the data.
M value: analysis of green probes, identification of adjustment variables
Percent Variance explained: 
PCs | Batch | Center | Day | Month | Year | Amount | Concentr. | Row | Column | Stage | Grade | Age |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2.2e-16 | 2.2e-16 | 1.6e-61 | 5.7e-39 | 3.8e-31 | 1.6e-19 | 6.9e-04 | 3.2e-02 | 2.2e-01 | 0.36 | 0.17 | 0.2778 |
Remove the batch effect:
PCs | Batch | Center | Day | Month | Year | Amount | Concentr. | Row | Column | Stage | Grade | Age |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 0.6857 | 3.984e-05 | 5.4e-01 | 6.9e-01 | 7.7e-01 | 4.6e-01 | 5.4e-02 | 7.9e-08 | 2.7e-02 | 0.649 | 0.033 | 0.881 |
Remove the plate row effect: