I don't know if any of this kind of stuff is out there, so I'm hoping some of you guys may have found things like these.

Applications/websites/online tools that help learners internalise sentence patterns

Example:
English sentence (progressive difficulty)
Drag-and-drop scattered and parsed Japanese sentence

And are there any apps/online tools to help learners develop stronger connections between Japanese verb conjugations and their English translations?

Example:
English sentence
Clozed Japanese sentence with input box for the correct verb ending (or drop-down list with several choices)

Trying to communicate ideas that I'd usually use the present perfect or past perfect for creates so much interference when I want to express these same ideas the Japanese way, among other lexical discrepancies that I may or may not yet understand. Overcoming these problems seems like a daunting task without these kinds of tools, but it's an exciting prospect in any case lol.

I know the 2nd exercise would be pointless without learning the different characteristics between English and Japanese verbs, but since I'm starting to realise these things now, I'd like to start thinking between L1 & L2 a lot more efficiently.

I started making a deck that kind of accomplishes the latter (e.g. front: 書かないだろう ・ 書かないでしょう back: "probably won't write" -- presumptive, negative, plain/polite) but I definitely don't have the programming skills in me OR the patience to create a card for every auxillary verb, let alone trust in myself to make more complicated sentences.

I'm hoping somebody has already enriched the public domain with this stuff or, perhaps, are working on it (shameless hint?)?

What you're asking is essentially what good textbooks do. JSL (Harz-Jorden and Noda), for example, has extensive examples of the patterns you are mentioning.

One problem with websites and programs is that you can never be sure that the information is accurate. With a good text such as JSL, you do not have this ambiguity.

If you feel like it, nothing prevents you from inputting the kind of examples you need from the text to Anki. I personally did that for a while, but I just can't stand the boredom of doing Anki reviews. YMMV.

Thanks, found them super cheap on ebay

Maybe I'm fussing over nothing, or expecting too much, but it seems that even the popular beginner guides (Tae Kim/Hugo Japanese/Visualising Japanese Grammar/Nihongoresources etc.) fail to provide some fundamental basics. All of the above seem to be lack any explanations of the semantic differences between English and Japanese verbs for example. I found this quite enlightening and somewhat of a breakthough, but I had to learn this on my own, and it's scattered all over the place. I often feel like I'm searching for explanations and would-be-obvious patterns without knowing what needs to be explained to me, so even with a collection of textbooks, I worry I'll still have to deal with this kind of uncertainty until I've stumbled upon enough puzzle pieces.

I guess it doesn't make much difference to the way I learn either way, but I agree that textbooks are uniformly better than websites. Thanks for the pointer on JSL, hopefully I'll be able to afford more books like those in the near future.