you really want to have a 3rd drive if you are going to raid or you partition the drives off before you set it up.
i haven't ran an array since i switched to ssd tbh but my last setup had 500gb f3 samsung drives, i had each partitioned off with the first 150 for the array and the rest as raw data. then once the os was installed i would format the rest of the space from dos and each would pop up in windows as its own drive. put the clone on there and it is easy to fix your os
tbh it would be much easier to put your clone on a 3rd drive, save so much hassle.
have you increased the pch voltages any?
it was something i had to do with each drive i added to to the array when i last did it dude. i had 4 in it at 1 point but tbh 3 was maxing out the controller anyway so the 4 went to waste anyway.
how long are we talking about it taking to start up? is it loading windows fine and then just not showing the desktop or taking forever to load up?
if it is an os issue it could be manythings you know, i would start with malwarebytes and see where it took me.