I am getting more pessimistic about doing a recording soon for Clarines and Malaguena as well. I spent some time working with the final exam piece, implementing some ideas how to make it sound more interesting and fresh, and as a consequence I haven't had the time to work with this lesson for the past few days.
Here's my take on your questions.
Malaguena 1: these pulloffs are the hardest part for me in this piece, because controlling the tone is so difficult. You need to alter the strength, speed and the angle of the pulloff depending on which fret you are pulling off from. At the higher frets generally you need to use more of a vertical angle and do the pulloff more gradually (ease the finger off the string instead of letting it snap from underneath the finger instantly) than when near the nut. Also, do not use the tip of the finger (where the callous is) for the pulling finger, because that will make the pulloff sound snappy. Instead, fret the string slightly below the callous. In my opinion, in order to make the pulloff sequence sound good, ultimately you need to practice each pulloff individually to make them sound of equal volume and tone. It's a lot of work, I'm afraid.
2: Have you tried p,i,m,i,m,i|m,i,m,m,i|i,m,i,p,m,i? This is what feels the most natural for me despite the index finger repeat between bars 63 and 64 (I rather take the repeat than the awkward double crossing). I also generally make a finger lose its turn when there's a slur in the alternation sequence, so that the i-m sequence stays in sync relative to the beats. Hence the repeat of m finger in bar 63. In general I think you should just find the most comfortable fingering for you without sacrificing the tone you want regardless of the difficulty level of the piece. Sometimes that means extensive practice of a fingering to make it feel more comfortable. I think often the discomfort at right hand fingering comes from the lack of finger independence, which then should be practiced so that the fingering doesn't feel uncomfortable anymore.
Clarines Y Trompetas: You are right that M. Delcamp omits the rests in the sense that he lets the bass notes ring over the rests. As far as the timing is concerned, he does take the rests into account. The reason he is doing that is probably to give the piece a better "flow". Often times the rests are used in the sheet music simply to fill the measures to their correct duration, and do not indicate the composer's wish to mute the strings. It is up to the performer to interpret the reason why a rest was added somewhere. Talking specifically about measures 33 and 42, indicating that the bass note should ring over from the previous measure would mean placing a tie across the repeat section, and that kind of notation, if not strictly invalid syntax, isn't generally used often. It's easier to put a rest in the beginning of the measure and let the performer decide whether they want to let ring or mute the string.
The degree of simplification used in the sheet music (as well as what interpretation means) became very apparent to me when I converted a polyphonic midi file that was created by playing keyboard, into sheet music with a computer program. The sheet was filled with ties, 1/64, 3/32 notes and rests in places where human sheet music writer would simply omit them for the sake of clarity, and as such was nearly impossible to read because of all the clutter. For example, lets assume that you as a composer want to play two chords each of a crotchet duration (and also lets assume that chords are identical with each other) . When you play the chords, there is always a tiny rest between the chords as you generally silence the first chord momentarily before playing it the second time. With legato playing the rest is just much shorter than other articulation types. This is just to show that sheet notation cannot be taken literally. Especially with guitar sheet notation there are lots implied and rules and conventions that the player needs to know by experience. When to obey the rests are one of those conventions, which are of course open to interpretation by anyone performing the piece.