I'm glad you got everything working for the most part on your laptop, obviously something is going on with your Desktop that I'm unable to help with. I can hopefully address some of your performance concerns, though.
There are some stuttering effects that occur in combat or during cutscenes, usually from special effects. This is caused by the shader cache, and it happens even without the HD texture pack. It's a persistent problem with Dolphin itself. There is a fix with the Ishiiruka version of Dolphin (Download, Ishiiruka Thread) in the graphics config under the hacks tab (you must be using the Direct3D backend, not OpenGL). The setting is called Full Async Shader Compilation. This can help lower or completely eliminate the stuttering caused by said effects. Ishiiruka is an unofficial build of Dolphin, however, so you may experience other issues not present in master. Be sure to report them in the Ishiiruka thread if you encounter any.
Besides the shader cache, the game / Dolphin is very CPU dependent. If I drop my CPU overclock from 4.5ghz down to stock settings, I can see a noticeable difference in the amount of stuttering. Also make sure to use the DDS versions as recommended, Dolphin has a much harder time with PNG at the moment. As far as settings go, increasing Internal Resolution over Anti-Aliasing with yield better visuals for the performance cost. Basically IR is much easier on Dolphin than AA and will give a better boost to visuals, so always increase your IR over AA first. I personally run at 4x IR, 4x AA, and and 1x or 2X AF. The lower AF is to make sure that Bruno's dynamic lighting textures work properly, if you turn AF too high you won't be able to see them due to how AF effects mipmap textures.
Edit -
For Bighead: I posted this a while ago, but it's basically a slightly more up to date and better organized version of the pack of dumps you have listed on the front page. I would prefer the one linked in this post to be the one people are downloading if they want to help out - Link.
There are some stuttering effects that occur in combat or during cutscenes, usually from special effects. This is caused by the shader cache, and it happens even without the HD texture pack. It's a persistent problem with Dolphin itself. There is a fix with the Ishiiruka version of Dolphin (Download, Ishiiruka Thread) in the graphics config under the hacks tab (you must be using the Direct3D backend, not OpenGL). The setting is called Full Async Shader Compilation. This can help lower or completely eliminate the stuttering caused by said effects. Ishiiruka is an unofficial build of Dolphin, however, so you may experience other issues not present in master. Be sure to report them in the Ishiiruka thread if you encounter any.
Besides the shader cache, the game / Dolphin is very CPU dependent. If I drop my CPU overclock from 4.5ghz down to stock settings, I can see a noticeable difference in the amount of stuttering. Also make sure to use the DDS versions as recommended, Dolphin has a much harder time with PNG at the moment. As far as settings go, increasing Internal Resolution over Anti-Aliasing with yield better visuals for the performance cost. Basically IR is much easier on Dolphin than AA and will give a better boost to visuals, so always increase your IR over AA first. I personally run at 4x IR, 4x AA, and and 1x or 2X AF. The lower AF is to make sure that Bruno's dynamic lighting textures work properly, if you turn AF too high you won't be able to see them due to how AF effects mipmap textures.
Edit -
For Bighead: I posted this a while ago, but it's basically a slightly more up to date and better organized version of the pack of dumps you have listed on the front page. I would prefer the one linked in this post to be the one people are downloading if they want to help out - Link.