Hi Mori, If head shows flat with straight edge it's flat. You're good.
Regarding your points & ignition system, that system works good. With practice setting points & timing is very easy. The 6CA plate makes it extra easy. Static timing done properly will be within a half degree of perfect. Well close enough for perfect running. We'll cross that bridge when we get there. Properly serviced points are extremely reliable. Proper service is not hard or time consuming.
My Tiger Cub has the energy transfer ignition & it starts easy & runs good. It has AC lighting & no battery. The lights are very dim at idle, that sucks. I started restoring cub some years ago & it still sits unfinished. I hope to get to it in 2019, seriously.
Make sure you have "keepers" on your rotor or store it inside the stator. This protects the magnetism. Left to stand alone the magnets will loose power. Many rotors get weak due to this. Of course they can loose from old age too, but no keepers is very hard on them.
Remember the PRT on the early bikes is different from wedding band bikes. So make sure you do PRT seals for your style motor.
Regarding motor install that's hard for me in any case. The motor is about 130#. Feels like 500 when your lifting it. No good place to grab it either. The pre 1970 frames are the worst in my mind. 1970 had the removable plates & OIF has the spacers to give some wiggle room.
I find it very easy to gouge front motor mount area on engine. Tape up the casting well in this area. The frame tabs are not so easy to line up on the front. I also think follow shop manual
& removing nuts, studs from lower rear frame is worth while.
The trans is fairly heavy. The clutch/primary drive is very heavy. The cyl. is heavy.
This go round on the '69 Bonnie I'm doing it different. I have motor stand so I decided to install cyl. on stand since it's much easier in my mind (at this time). I installed trans & outer cover since it was easy on stand.
Leaving head & primary drive off. Still rather heavy.
One reason I did trans before install is shift fork rod end is open on left end. This was a source of leakage. I wanted to seal over the end with silicon after trans was assembled. Very hard to access this area so I wanted to seal it with motor out. I turned motor on end to do this. Easy while on engine stand.
Made lifting handle. I took a piece of angle iron 20" long drilled it such I can place old head gasket on cyl. Then bolt angle iron handle to rear outside head bolts. Idea is to use as lifting handle to ease motor in.
Then taking some long bolts & installing on rear motor mounts where side plates bolt. These will be rear lifting handles, but main weight is held by angle iron.
I don't know if any of this will work yet. But 2 old farts just grabbing motor is too hard. I needed to find a better way. I have a chain hoist for pulling car motors, but no good way to attach to Triumph motor. A tiny cherry picker might work??
The head bolts are not all that easy to install with bike in frame sometimes either. But if motor is not fully bolted you can cant it over slightly which helps.
I'll let you know how it all works out in a few weeks with photos. That is photos if it works good....