There's no substitute for flying. Simulations assume ideal conditions. The efficacy of construction techniques becomes apparent after you've flown a bunch
A great source of information is The Rocketry Forum (TRF). Have you found that web site?
Speed when the 'chute opens
You are correct that the speeds you're quoting sound high for a separated rocket of the Zephyr's size. I usually aim for a descent rate of less than 90'/second prior to main deployment. 15'-20'/second when under the chute and landing on grass.
JB Weld
JB Weld works fine for fine fillets, though it's overkill for a rocket of this size. Wood glue is fine for attaching the base. In fact, it or regular hobby epoxy would've been fine for the rest of the rocket.
Motor Retention
I don't recommend masking tape, even for the G motors. It's too unpredictable. My favorite commercial retainers are from AeroPack. Estes also makes a good 29mm plastic retainer. Those may be impossible to install since you've already glued the base together. In those cases, I've made motor retainers using threaded inserts, wing screws, and washers. TRF probably has some articles on this.
Chute protectors
I wouldn't expect holes in a well-made chute protector after one flight. Frank is correct that you can add an additional layer of production by adding dog barf (aka fire-retardant cellulose) under the chute protector.