Hello! It sounds like a wonderful trip to Bhutan that you are planning, covering Thimphu, Punakha, and Paro. Here are some tips for your journey.

Best Time to Visit:
The best time to visit Bhutan, pertinent to Thimphu, Punakha, and Paro, is during Spring (March to May) and Fall (September to November). The weather is pleasant and the valleys are blooming with flowers.

Route and Accessibility:
Flights are available from major international cities to Paro, the only international airport in Bhutan. From Paro, you can travel to Thimphu via road which is approximately 1.5 hours away. Punakha is about 2-3 hours drive from Thimphu depending on road conditions.

Accommodation and Booking:
Accommodations range from luxury hotels to homestays in these cities. It's recommended to book your accommodations, and also plan your itinerary well in advance through a Bhutanese tour operator as per government regulations.

Clothing and Essentials:
Pack warm clothes, a sturdy pair of hiking shoes, sunscreen, hats and sunglasses. Remember to include rain gear as weather can be unpredictable. Carry essentials like a torch, medication, water purification tablets and energy bars if you plan on trekking.

Health and Safety:
Ensure to follow only marked trekking paths for safety. Undergo a thorough health check-up before the trip as the high altitude can impose issues for people with certain health conditions. Drink plenty of water to avoid altitude sickness.

Local Etiquette and Respect:
Bhutanese are generally very warm and respectful. It's required to remove your shoes and hats before entering a religious place. Modest dressing is appreciated. Respect local customs and traditions to ensure a harmonious experience.