Alcast's builds are maximized, but they can be a little clunky. His magblade has four buffs on the back bar that need to be reset every eight seconds...that does feel like a tough rotation. If you're not running vet trials, I'd personally simplify things by exchanging crippling and twisting path for entropy (for the major sorcery, unless you have another source) and moving siphoning attacks to the back bar. Then it becomes like a 20 second rotation or an emergency bar for harness magicka. I'd then bring concealed weapon onto the front bar...it is cheap, fast and powerful and will offer some dps that'll help you maintain resources a little better.

Regardless, to your specific questions:

Merciless Resolve: this is a tough skill to master, in part because it doesn't work well a lot of the time. I find it helpful to turn my buff bar on so I can see the timer. Then I consider its main use the damage buff...the spectral bow is just sort of an occasional benefit. But what I try to do on my magblade is merciless...light...heavy...rotation. In other words, I try to weave a light before every heavy, which usually gets the astral to proc pretty quick. They considered recent changes to this a "buff," but honestly between how they changed it and some changes to targeting its become harder to use and quite annoying...you're right about that.

Magicka: if you're using siphoning attacks and merciless, you should be getting in plenty of light and heavies to keep resources up. You might need to focus on more heavies...they take forever, but the damage and resource return make them something to use often.

Alcast's build and your setup are a starting point...they're adjusted for max power and minimum resource management. If you can't get the resource sustain you need through abilities and heavies, you can start adding magic recovery glyphs to your gear. But before you do, there's a good way to test how much this will help. If you're running the apprentice Mundas (spell damage), go flip to the Atronach and test your performance. The values aren't exact, but they're close enough to the difference in a magic recovery vs spell damage jewelry glyphs that you can mostly gauge how much power you sacrifice and how much recovery you pick up.

But the core issue with the build is that you're geared for all power and no recovery. Given the reality post-Morrowind, that's going to require either adjusting your playstyle or some gear changes. Note that Alcast's guide lists the jewelry as spell damage, but then he says he was most comfortable running two mag recovery glyphs on this build.