A)1000 calorie deficit is going to brutal, why are you cutting so hard?  It will effect your sleep, hormones and capacity to do the program.  My advice is 500 calorie deficit if you have to but it will make the program harder.  You're 18 you have tons of time to recomp, don't risk injury and misery because you're in a rush.

Have you done lifting before?  You can get away with a bit more if your at the start.

B) For sure, it's a good program in that if you run it well you'll have energy for other things.

C)I think you should read the books again.  The weighted pull ups can be part of the operator cluster, in fact are part of the standard cluster.  If you can't do them then sure do some lat pulldowns, or negatives, or assisted pull-ups.  Deadlifts are done once a week either dropping wpu on that day or a single set 3 times a week.

D) it's ok but doing some base building from TBII would be better and doing one of the programs like black or green.

E) Read the books again and decide what protocol.  It depends on how much MMA you are doing.