It doesn't seem likely that a bent linkage would affect one gear and not all. Popping out of 2nd gear is more likely to be related to worn dogs on that gear.

 

Well, it's not an absolute... I'd certainly make the effort to straighten out the linkage to see if that fixes it. That's far easier than transmission work.

 

That's a big job. The engine has to be removed from the bike and the cases split to work on it. It's practically an overhaul.

 

how long have you been riding? the reason i ask is that while a lot of the time, the second gear issue is fully the dogs on the second gear's fault, many times it is a new and inexperienced rider not giving second gear enough kick resulting in it not seating correctly. if this is your first bike and you are a new rider, this may be your issue, especially on these bikes because they have a cable and not hydraulic clutch. however, if you know what im talking about and this is not your issue, then the easiest way to check the dogs without splitting cases is to support the weight of the bike by the frame (engine picker or shop crane works good), remove the fairings, full exhaust system, clutch cover, clutch, external shift linkage, shift drum, and then pull the oil pan. once you get the shift forks that will be sitting free at this point pulled out of the way, you will be able tin inspect the dogs on the mainshaft. 1st/2nd gear is going to be the medium sized gear in the middle of the front shaft (in relation to the bike). if you get a manual, it will explain it better, but that is the way to inspect without removal and complete disassembly of the engine. if you find that they are worn, this will require case splitting and gear replacement. it can be done, and isnt as daunting as some would have you believe. you can pick up a good used set of trans gears for about 100 bucks on ebay, and have the job done in about a weekend if you have no experience but are good with tools and books. with gaskets and parts and incidentals like new oil/filter, you are looking at about 250 bucks if you do it yourself. good luck and let me know what you find. if you get as far as checking the gears, take pictures and im sure either i, or someone else will weigh in for you.