Thanks for your query,based on the facts that you have posted it appears that you have post void burning and post ejaculation pain in your urethra
This is most likely to be due to either infection of the prostate
or seminal vesicle
which is confirmed by presence of pus cells and agglutination of sperms.
Please consult qualified Urologist
for clinical assessment.You need to take long term course of antibiotic like Doxycycline for 6-8 weeks.