Okay -- so here's something VERY important.
IF you have a flat tappet cam -- cranking over the engine and starting it etc WITHOUT proper cam break in - is really asking for trouble (flattening the cam). This break in procedure is even more critical with todays oils. The reason it needs to be started and then brought up to 2500 rpms or so - is to splash oil on the lifters/cam lobe. Without that critical oiling and break in - you risk a problem down the road.
THIS is not a problem - and not required - if you have a ROLLER CAM.
Okay -- Starter motor had to have big torque applied to it to break an ear like that. There are clearances for proper starter motor install. I can't remember what they are exactly but I'm thinking .040 between the flywheel teeth and the starter gear - someone jump in here and correct me if I'm wrong. Lacking that - do some research and check what this figure should be. There are SHIMS that might be needed between the block and the starter motor mounting face. There are also special bolts that must be used -- they have a knurled shoulder on them.
ALTERNATOR:
On a ONE WIRE alternator - there is no need for the RED wire loop even though it's shown in the wiring diagram. All you need is ONE wire for charging. The PIX also show a brown wire == I ASSume this is going to a volt meter?? You don't need that either. The volt meter can come off any 12V + "hot when switched" wire - and will read the system voltage.
I would make sure that you have GROUNDS from the battery to body/frame/motor. Remember that the ground (-) is every bit as important and carries just as much load - as the positives! It's all part of the circuit. Make sure you clean the area between connections to BARE METAL. Don't use the motor mount as a ground - it's RUBBER between the frame and motor -- if you do -- I loop the ground between the frame bolt and the motor side bolts.
Have your battery load checked. If it's been sitting for awhile - it could be low (and the alternator is really trying to pound some amps back in it) or be "sulfated" - or you could have a bad cell not taking a charge - and that might make the alternator try to overcome this... but shouldn't (IMHO) as the alternator is internally regulated.
When you say the alternator is getting "hot" -- explain what your idea of hot is - or what you're observing.
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