Hi and welcome. Good to know you have done ok so far getting things set up. The last fellow before you was less than encouraging.
I need a little more information to know what's going on with the real shelter. First check is what's the date on the download, have not checked the mod for a while.
What do you mean by "transitions not working well". The rain will look different. Lots of progress has been made to get things looking decent and close, but with this script heavy pack, there will be a noticeable hesitation (100~200 ms) for transitions. The mod author has worked wonders getting things optimized, comparing to how it was before. There are a bunch of settings that can be toggled in game, and several in the setup of the mod, to work out "most" major bugs. I remember seeing an experimental rain texture patch somewhere that can be enabled if you are having problems.
Are you doing the Real shelter last? I know lots of stuff (requiem for the indifferent.esp, and DynDoLOD
say they should be the last esp, but real shelter is the real last esp. worth checking:)
Also, what is the system you are using. Anything less than an i7 4 core with ~4.00 Ghz and a 900 series of better graphics care will struggle (you will unfortunately have to install the low Rez options in STEP
Extended, choose the low quality DynDoLOD
option, and the performance ENB options). Probably should put that as a proper note somewhere on the main page's wall of text :)
Hopefully this is an easy one to sort out. If you care, please do some benchmarks, primarily FPS. Some people have reported (my brother one of them) that they only get 30 FPS in some area, like marcarth and whiterun. The ENB settings I give are mid level, so if you get low FPS the first thing you want to do is go back and reinstall with low settings (should not even have to re patch anything either). That should give you lots of FPS if you pick the performance options.