We plan to conduct a clinical trial of herbal product. What are the guidelines?

Department of Ayush Gazette Notification 2008 guidelines for evaluation of Ayurveda, Siddha, and Unani Drugs and other traditional medicines of India describe the approach for different formulations as per following categories:
I Ayurveda, Siddha and Unani drugs
II Patent or Proprietary Ayurveda, Siddha and Unani drugs
III Indian ethno-medicines based drugs not covered by I and II
IV Medicines based on extracts of medicinal plants of India
For each category, depending on 1) novelty of indications 2) available evidence / experience, the guidelines recommend animal pharmacology, toxicology and clinical trials.
The clinical trial has to be done as per GCP guidelines. Dept of Ayush has prepared GCP guidelines, which are formulated based on CDSCO document on GCP guidelines for clinical trials on pharmaceutical products. They should be followed for carrying out all ASU medicines / other TM research in India at all stages of drug development, whether prior or subsequent to product registration in India.
The following data are required for clinical trial application:
Information on formulation
Experimental Pharmacology
Safety data
Investigator brochure
Protocol
Patient Information sheet
Informed consent form English + Local language

What are the guidelines used for conduct of the diagnostic pathology lab audit?

Please see (1) ICMR GCLP guidelines of 2008; (2) US FDSA Compliance Programme Guidance Manual of Bioresearch Monitoring Programme (BIMO) for GLP Compliance Programmes for non-clinical labs. Additionally, it would be worth checking NABL website.

For methotrextate bioequivalence study, the US FDA recommends that the study should be conducted in patients with mild to severe psoriasis or rheumatoid arthritis (RA), who are already on established regimens of 2.5 mg every 12 hours. What is the time line for established regimens?

There is no fixed regimen for methotrexate. Most clinical trials describe the duration of treatment as 3-6 months. American College of Rheumatology quotes:
Time to effect
Improvements in arthritis and other conditions usually are first seen in 3-6 weeks. The full benefit of this drug may not be seen until after 12 weeks of treatment.
It would be better to ask USFDA what they consider as "established regimen".

How the drugs should be dispensed for injectable bio similar studies that are double blinded?

In order to maintain the blinding in this study, only a pharmacist (or a designate not involved in study drug administration) should know in which arm of the study subjects are enrolled. The pharmacist (or designate) will provide either test or reference product to the investigator (or designate) in a syringe that will be labelled with:

• Subject ID number
• Subject initials
• Protocol number

In order to maintain the blinding, only the pharmacist (or designate) will have access to the randomization list. All subjects and all study staff except the pharmacist (or designate) will be blinded to the arm of allocation for each subject.
It would be desirable that the pharmacist dispenses IP for 1 subject at a time

Can a govt hospital doctor conduct trial at his private set-up. EC is independent. What are consequence of such case?
If government doctor is officially allowed private practice, the doctor's private clinic can be a site and the trial can be approved by independent EC.
However, it is important to decide how and where an SAE will be managed. If the SAE will be managed in a private nursing home, the doctor can handle it himself. If the SAE is to be managed in the government hospital, where he is employed, there is a risk of questions coming up from the government hospital / EC etc. If the SAE is death, the situation will be quite serious.
If the government doctor is not permitted to do private practice, then he cannot conduct a trial in a private clinic.