Hi Mike,
As I said, I lived in Panama for five months and have had spent alot of time on pipeline road... it is really incredible...
Here's me advice for that area:
First, to get to pipeline road ask someone to take you to the Smithsonian Barro Colorado boat launch. The gravel road near the boat launch continues parallel to the canal and if you follow it you will reach a gate that marks the entrance to pipeline road within 5-10 minutes. First though, check out the marsh that is opposite the canal about 100 meters back down the road from the boat launch - a good place to spot water birds such as herons, Jacana, and even Capybara (if you are particularly lucky).
Now for pipeline road....
When I left (in June) they were expanding part of the road to build a second canopy tower... the construction covered the first 4 km of the trail and the noise and widening of the trail diminished the viewing... also, high tourism traffic at the start of the trail makes it hard to see alot of rate birds... however, this should not discourage you because the rest of the trail is excellent. Pipeline road does not have any major sidepaths except for a new road that was built off of it that goes to the site of the new canopy tower. This is about 1 1/2 km down the road. When you find this fork stay to the right and you will continue down the original pipeline road. Now, once you clear about 4 kilometers you will be well past the construction and most other tourists.. you will only run into hard core nature lovers and Smithsonian researchers past this point. ALWAYS take a good look down the rivers/streams when you pass over them (I've seen some great stuff down there) and be cautious on the bridges... some are rotting, but still crossable with care. Personally, I think the best viewing is past Rio Mendoza (8.8 km down the trail) as this is where the trail narrows and virtually no other people will be present. Also, the mammal and frog viewing along this path is excellent! Between 6 and 10 km down the path I have seen a plethora of wildlife including Peccaries, Ocelot (on one special occasion), Tayra, many trogons, a Harpy Eagle, sunbittern, tiger herons, and many other species. Just watch for snakes and bring plenty of water. If you go at night or near dawn or dusk past km 6 you have a good chance at seeing some mammals...
Be very careful about leaving the path when on pipeline road... you are safe on the path but there are pit vipers in the bush and if you get bit far in you will be in serious trouble.
If you do leave the path keep in mind that there are Fer de Lance pit vipers on the ground but also Eyelash pit vipers hanging from vines and lianas so watch yourself!
Lastly, if you are seriously into birds I highly recommend getting a flight over to Boquete and going to Vulcan Baru National Park.. it is incredible and you can see Resplendent Quetzals there and some rare volcano birds on Baru.
Hope that helps, if you have more questions post them and I can let you know all about Panama... I've visited nearly the whole country...
-Andrew