This is from the very link that you yourself provided..... " Lykken is in prison serving an unrelated 227-year sentence for rape and kidnapping."
Nor was the victim his wife.
Here is a little better info on the "nothing else" Lykken was convicted of http://law.justia.com/cases/south-dakota/supreme-court/1992/17478-1.html
What he was in prison for had nothing to do with the murder charge they tried to pin on him. That was the point. These things do happen, and largely they happen because of how the system works.
But getting to Lykken's case (the one he was in prison for), do you really think that warrants a 227 year sentence? In the facts of the case, presented in that appeal finding, the conviction depended largely on the credibility of the victim. She claimed that the act was non consensual, he claimed it was. There are some significant question marks however. Firstly, she claimed that she woke up with him sitting on the end of the bed. But there was no sign of forced entry and she claimed that the doors were locked. So how did he get in? Secondly, they were not alone in the apartment and this supposedly happened over a number of hours. It seems unlikely that a ruckus going in the next room would not pass unnoticed. Then there are the subsequent events. For example, not calling police immediately, but instead calling friends the next day who then advised calling the police. Also, the encounter between the victim and Lykken the following day. IMO you could plausibly argue that all is consistent with him being there by consent, but at some point in the night things went south and some sort of conflict happened. Which is different from her account. You should also keep in mind that in her prior divorce proceedings, the victim had admitted to committing perjury, so not being fully truthful in order to achieve her own ends is not an alien concept to her. Her version of events may not be fully accurate.
Then there is the nature of the charges and how they considered the evidence. The argument that "kidnapping" was a discrete and separate element from the rape IMO is complete nonsense. We all know what kidnapping is, and to apply it in this context is playing games with the letter of the law, twisting it to serve a purpose it was not intended to serve. And in any case, the facts underlying both charges are identical, so even if you accept that they are different, the sentences should be concurrent, not consecutive. The kidnapping charge appears to have been included for the sole purpose of ramping up the sentence on a conviction.
There are two possible explanations for why they would have gone for such a lengthy sentence that is substantially out of proportion to the crime, particularly considering the doubt that exists regarding the accuracy of accounts. Firstly, this Lykken guy appears to be an unsavory character. The local LE/DA may have decided that this would be an opportune time to remove him from the community for good, so they stretched things as far as possible to achieve that. The other possibility is that he was overcharged in an effort to get him to plea down and avoid the cost of a trial. They get a conviction, case closed and everyone is happy (except Lykken). But when he maintained that he didn't do what was being alleged, they made an example of him and got him the max, to serve as a message for future cases of what happens when you don't play the DA's game. The next guy coming along is not going to risk maybe getting 227 years in prison, and instead will take the 5 years in a plea bargain. The risk of fighting back for a poor person is simply too great if that is the price they could pay.
You have to kind of wonder, if the local LE/DA were so willing to try and pin a murder rap on Lykken on what must have been clearly flimsy grounds, how sure can we be that they didn't do the exact same thing in his original case?