Should have been about 2 hours

You're not "wrong" about any of these things, but I thought I might share some info. and commiserate with you a bit.

1) Remember, Del Toro was leaving small clues behind, like the discarded construction hat on the sidewalk that tipped off Jones as to which street to start down. Also, Tom Brown Jr. (the tracker on whom the Jones character was loosely based) has talked of there being a sort of "tracker intuition" that allows the pursuer to infer probable behavior of the pursued. This intuition comes from years of tracking and is far from foolproof, but would explain how Jones sensed that Del Toro had doubled back on him.

2) One source (I've forgotten who, my apologies) has it that the final wilderness chase was supposed to take place over several days or weeks, which makes for the construction of elaborate dead-fall traps much more plausible. It also makes more sense in regards to the knife construct, too. If you're WELL practiced, you could probably flint-knap a knife in the hour or so it appears to take in the film, but good luck forging a blade out of scrap metal with NO TOOLS in an afternoon......

3) I think we're supposed to understand that Del Toro is not really leaving a super-obvious trail -- rather, the tracks have been amplified in many scenes so that the camera and audience can understand the tracking experience better. It seems unlikely that filmstock could capture the faint trail of moccasin prints across the ground in any meaningful way for moviegoers unfamiliar with tracking. I must say that the Canadian TV show "Mantracker" uses an interesting way of doing this -- the otherwise-difficult-to-see tracks are made to glow in post-production.

4) No explanation for this one. All I can say is, that when I first saw the movie, it didn't really bother me because I assumed that the train was just starting to move forward after having stopped at that overpass-station. But even so, it should've gained full speed long before Jones could've caught it.

5) Yeah, the suspension of disbelief is stretched pretty thin in the climactic fight, but this is what I think we're supposed to understand: Jones misses injury in the waterfall in part by sheer luck and in part by his skills in wilderness survival (i.e. keeping your wits about you and staying afloat in rapids); the adrenaline rush, combined with the shock and vaso-constricting effects of the freezing water help numb the pain and quell the blood loss that each character's injuries caused; Del Toro's arm wound was in a major artery, which is why he could fill his cupped hand with blood so fast, and why he is shown applying the knife-fighter's tourniquet to his arm moments later. The only comparable wound Jones suffers is near the end, also in his arm. I don't recall Del Toro leaving a blood trail from this - Jones simply follows the path they were on along the rocks. It's the only way he could've gone, barring jumping into the water or scaling the cliff straight up.

To conclude, I'm sorry that these "movie exaggerations" spoiled some of your enjoyment. I found that they were so minor compared to the real groaners you see in typical mainstream action films, I actually didn't mind most of them at all. I hope you can still focus instead on the positive qualities of the film, including the most comprehensive and realistic portrayal of tracking in movies (to my knowledge), and very realistic Sayoc-Kali knife fighting. If 2 expert knife users dueled it out, no holds barred, it would very much resemble this type of fighting (except it would be over much, much quicker, and the fighters wouldn't bleed like they were blood-filled water balloons).

But thanks for the post. Glad to see interest in this film!