Hi Zandit, yes ebony timbermate is the darkest I think so use that for a black stain. Be careful when you are fitting/removing the neck - the timbermate being on an edge will break off very easily. Clear coats should give it a bit more strength.

Yes the tall lug on the output jack will touch the jack tip. Once you have moved the lugs plug a jack lead in to make sure the tip isn't too tight to remove and the hot lug (short lug) is well away from the lead shaft/tip.

I wouldn't use ebony timbermate on the spalted veneer, you will cover up too much character. I usually leave the small cracks and crevices as they are - not worth risking sanding through the cap. A lighter colour timbermate may work.

Once you have done the mock build please post the distance centre of 12th fret to both E string saddles. Align the ruler in a similar alignment the string would go. Wind the saddles as far forward (toward the nut) as they go for the measurements.