The protocol is not ok for what you want i would suggest a few modifications.
Your cutting staining protocol is controlled by how you would analyse it. I would suggest stereoligical quantification.
1)Perfuse animal with PBS (mouse 30 ml, rat 100ml)
2) 30 ml 4% paraformaldehyde 4ºC, block the brain, in vivo post fix for two hours at room temperature (r.t.)
3) allow the brain to sink in 30% sucrose in PB for 48 hours. Snap freeze. then either cyrosection onto slides 20- 30 micron or cut for free floating 30-50 micron. Never let the tissue you are sectioning touch the oct.
4) wash sections in 0.1M Phosphate Buffered Saline (PBS) (pH 7.4) with 1% TritonX100 (3x 5 mins)
5) with GFP never use unmasking (hcl or citate)
6) block wiht 0.1M PBS (pH 7.4) + 1% TritonX100 + 5% normal goat serum if secondary is raised in goat or sheep(1hr i)
7) prior to incubating overnight (4ºC) with anti-GFP in the same solution but 1% ngs
8) Wash 3x then anti GFP secondary for 3 hours. Very impt if you want to quatify.3x wash