1. To get around the RC ActiveX issue with Chrome just install ActiveX for Chrome. No more manual download/run issues just works like it does in IE.
2. If you get the "Not from Chrome store" message when trying to install the plug-ins for KLC just open your the Extensions page in Chrome (Tools -> Extensions) and drag and drop the .crx downloads onto the page. It allows you to install the plug-in manually.
3. Never experienced that one.
I gave up on trying to get IE to work consistently in Kaseya. Settings that allow on installation to work wouldn't necessarily work on the next workstation. Our support team uses either Chrome or FireFox for the most part. I think there are a couple guys that have IE working for them.