Macara border is a good option
In case it is of use to anyone, the border at Macara (south of Loja) is excellent. The frontier is a bridge and all imigration and aduana offices are located at either end of the bridge. The whole process took half an hour.
This crossing was completed (from Peru into Ecuador) with my bike on the back of a truck due to a knackered voltage regulator (2 new batteries fried to crisp in 2 days!). There is an aduana officer on the ecuadoruian side called Miguel Murioz and he is an absolute star - he rides bikes and seeing my bike on the back of a truck, he phoned a mechanic in Loja and gave me directions to his garage. He was so busy talking bikes with me that the agent processing my paperwork had to keep interrupting with questions about the bike detailsand in the end gave up and just filled in everything himselffrom my registration document!
A word of warning about northern peru - the cops on the PANAm are everywhere and we were stopped severaltimes, especially arounf Trujillio. Once we were done for speeding (the fine went from $100 to $20 with some haggling, though I think he would have accepted less....  !). I was asked for insurance on several occasions, but got away with my argentine bought policy. This is not valid in Peru, but my papers seemed to satisfy them and I got the impression they didnt know what they were looking at.
The stretch from Lima to the border is the longest ive spent on the Panam, and it is easily the worst part of the trip so far - avoid it if you can!
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