Fineliner pens are only hard requirements if you are submitting for official critique which in this case you are not so using a pencil for a few exercises isn't a big deal (although it is recommended that you use pens anyway). Regarding your second point it's fine to upload the ghosted planes with ellipses already on them as many people have done that before.

Lines: Your Superimposed Lines look great in both pen and pencil! Not much to say about that. Ghosted Lines aren't that bad either only a little bit of wobble in a couple of lines. Now for Ghosted Planes you didn't have to make separate pages for this exercise and the Ellipses in Planes, as you could have taken a picture of them before you added ellipses or taken a picture with ellipses on them (either way works). But I am mentioning this because in total you ended up with 3 pages of Ghosted Planes which is more than what is assigned. This is considered grinding and Uncomfortable explains why we don't grind out exercises on this page here https://drawabox.com/lesson/0/3/grinding But you did great work on this exercise so good work!

Ellipses: On Tables of Ellipses I think you improved as you went along with this exercise. The ellipses look a little more smooth and confident on the second page. I think you should practice drawing through your ellipses just 2 times (3 times is fine but 2 is ideal so that your ellipses look less messy). On Ellipses in Planes, your ellipses look really messy and some of them are clearly drawn through more than 2-3 times. On Funnels, some of your ellipses are misaligned with the minor axis. Keep this in mind when you practice these exercise in the future.

Boxes: On Rough Perspective, you showed improvement throughout the exercise but you forgot to do the line correction method so I'll request that you do one more page with the line correction method done for your boxes. You made a good attempt at Rotated Boxes, but I'm surprised at how small you made your boxes. I recommend when you come back to this exercise in the future that you make the boxes bigger. I think your pages for Organic Perspective look great! I won't critique you too much on these last two exercises since they are difficult exercises and you'll improve on drawing boxes in the 250 Box Challenge.

I think you should do one more page of Rough Perspective properly with the line correction method done. After you submit that I'll see if you're ready for the 250 Box Challenge. Take care!