so... little late to the party so forgive if it's been addressed... but at 1 1/4" that's going to be rough afa clearance. I think a 5 - way switch might just sneak in there but a tremolo is usually going to require 1 1/2" minimum unless you get something really low profile like used in the sabre series.
ok, that out of the way... jem - cool. is on my bucketlist to build a jem. have a 77fp. one of the best guitars I've ever played, and easily one of the best sounding guitars ever.
best neck finish: well... best for feel in my experience is tru oil. just feels like a raw neck despite offering pretty good protection. best for sealing/stability - probably poly. necks that are well sealed tend to fluctuate less with the humidity and for some this is a huge thing... others a small thing.
decal - have an inkjet or laser printer? get some clear waterslide decal stock. You can whip up the logo of your choice, print it, spray a few light coats of clear acrylic on it... and slide it on just like a model airplane. if you want to get fancy... you could print it out reverse, paint in some details with gold paint marker, add clear add very light clear, flip it and slide on. or... you can try your hand at screen printing. you can get screen/ink from many art stores as well as paper you can print, apply chemicals... and parts that aren't printed will dissolve. stick to screen... and you can squeegee on a logo.
lots of options anyway.
body finish - well same as neck... tru oil is just the best for a raw feel imo. osmo poly x raw is another I've learned from folks here that is just great.