I'm Brad - most people on here refer to me as "VBM."
Some thoughts/ideas you are free to dismiss :D !!!
I stayed at L1 until I could do the D3 workout under 5 mins with no subs. The usual sub for pullups is 3 bodyrows = 1 pullup (or 3 assisted pullups.) Instead of doing knee pushups try doing pushups with your upper body elevated (like hands on a stair and feet on the landing) to better mimic the plank portion of the pushup.
I'm not sure what your rationale is for jumping around the levels - it's up to you.
If your long-term goal is to get to the CF workouts, have your boyfriend show you the overhead squat with the PVC pipe and get to doing those pretty quickly. Also, try a super-scaled down crossfit WOD now and then.
View my log from the beginning. Find others with substantial amounts of posts and go through them. They should give you patience and perseverance.
Cheers and keep working!