Hi Adyan,
I think I have fixed the issue by myself after deleting some lines and just ending the Julian day on 366th day by keeping the simulation period till 2024 and not 2025's 212th day.
I still started the simulation from 2001's 32nd day tho. With 3 years of NYSKIP, making it 2004's 32nd day to 2024's 366th day.
I also deleted the two lines from spe_extract for the second variable but I know for sure that I deleted these two lines the last time and it didn't work.
The problems are so arbitrary sometimes. Thank you for your time and effort in replying but for now I think I have solved the problem. And, I would post what i exactly did to fix it, in a bit, if I can (for others who might face the same issue someday).
Sincerely,
Ashwin