Well, i finally did it. I spent a week in Bogota choosing and buying used bike and one week more in the surroundings of Bogota while they were doing all the paperwork.
So, personal experiences. I have a very basic Spanish, by the way.
Registering in RUNT really takes 15 min (and costs 4$). That was the easiest part.

Choosing the bike. I've read that bikes here are in awful condition and sellers don't negotiate too much... But it was a bit hard to believe. It's time to confess that i've never seen such bad bikes for such a bad price. After looking to 5 Yamaha XTZ250 (Tenere or Lander, they are basically the same, Tenere is more tourer type), bargaining the price down at maximum 300k peso, i decided to give up and buy a new Honda XRE190 (i didn't like it though). But before to have a look to the last Tenere in my list. Magically this one was in ok condition. Only one owner who did the maintenance at the mechanic shop and didn't even knew where the air filter is located on the bike. I was lucky. Upon a cup of tinto the price was negotiated from 12 400 000 to 11 800 000.

Transfering money. We decided to try swift bank transfer but 1) it takes 2-3 working days, 2) there were things i couldn't understand. For example, the client service in the seller's bank Bancolombia said that he can receive transfer in dollars even if he has an account in pesos but swift simply does not work this way... So, we went to a shopping mall and here in the ATM of Davivienda bank i received all those millions... Davivienda has no fees, ok exchange rate, 2 000 000 max for one transaction and unlimited transactions per day.

After that we went to SIM (the same place where you get RUNT). But before that the seller said he hasn't paid taxes for 2 years (although earlier he said he had, "al dia") but would pay them now in front of me. So we visited Bancolombia before SIM.The price of transfer was completely on him. It was on Thursday and i was told to return to SIM for my tarjeta del propietario (the card of the owner) on Tuesday. Because it takes time for tax information to go through a system. The seller gave me the keys, his SOAT (insurance) and Tecnomecanica for the bike and also his tarjeta del propietario. He said, i can drive now with his card. I don't understand how it works, really. But with his card i was driving for a week and no one stopped me. On Tuesday nothing has been ready yet. Came back on Thursday. Success.

So, one more advice: if you like a bike and decide to buy it, always ask for the papers for taxes, SOAT and Tecno. They're quiet expensive if buy it separately. Tecno costs 130 000, SOAT about 500 000 (for a year and you cannot buy one for a month) and taxes - depends on engine cc, 400 000 -- 500 000.