Hi Jack,
Welcome to the forums and it's great to hear you're enjoying your first foray into composites with the skinning kit. Skinning is definitely an art and a skill and, ironically, one of the more challenging techniques to master in the world of working with carbon fibre. If you can perfect skinning then you're well set to work with carbon fibre in other ways too.
You mentioned that you're struggling with the 3rd application of the XCR coating resin and that you're getting some air entrapment at that stage. This would be most unusual and hard to explain because you've already indicated that you don't have any problems with the 1st or 2nd applications. Since there should be no difference in the material or the process for the 3rd application then we can say with confidence that it is a reaction to something that you're doing between the 2nd and 3rd application. From what you've described, I'm really struggling to understand why you're doing what you're doing after the second layer. With skinning you have two options for each new application of resin, either apply the next coat when the previous one is at the 'b-stage' or - if the previous layer has fully cured - 'key' the previous layer with abrasive paper (scratch the whole surface) and then apply the next coat onto that keyed surface. There are no other options which will ensure a good bond between layers. There's no reason in the skinning process why you would ever want to wipe the previous layer with IPA or window cleaner! If the previous layer has fully cured then it needs keying, then just wipe the dust away and on you go with the next layer. If it's not fully cured (is at the B-stage) then you just apply the next coat directly onto that previous (tacky) layer.
For what it's worth, the reason IPA and/window cleaner are causing the problem will be because the resin you're applying them to is not fully cured. Your IPA is likely to contain water, your window cleaner certainly will (as well as vinegar/acid) and the vulnerable - not fully cured - resin is absorbing some of the this water and vinegar. Then, when you apply your next coat some of this water and cleaner is contaminating your last coat.
My advice: stick to the process recommended in the guide; apply the 3rd coat at the 'B-stage' of the previous coat, directly onto the tacky resin. Drop the window cleaner and IPA and you should be fine.
Good luck! - Post some pictures

Matt
Matt StathamEasy Composites / Carbon Mods - Technical Sales