Lay the bike over to assist, if you want.
Use a piece of uncooked spaghetti

or a piece of wire to slide the spring down into the hole.
Grease for the ball, yes. On a dowel or similar. Or a piece of garden hose to send the ball down to the hole.
They should stay there if the bike's on it's side.
Grease on a big screwdriver to set the 'plug'/retainer. Plug to be approx .5mm below engine case.
I'd prefer to 'raise a bur' to retain the plug because I have no experience with red loctite in this application, which would require precision.
I burred over? just one corner, of one of the slots in the engine case. No pic sorry. A tool of suitable size and weight with a good hard sharp corner to contact the engine case. One tap might do it, maybe two. The bur does not need to be big. Just enough deformation to prevent the threaded retainer from backing out.
Check the bottom of the bypass hole, where the spring will seat. It shouldn't look damaged or uneven, imo.
Someone's been fiddling there if the retainer is screwed in too far. A bit like the phillips head screw on top of the tranny gets fiddled with!
You could have probably left it all together and just backed the retainer out. If done carefully, you could feel if the oe 'staking' was still effective by the retainer tightening near the engine case surface. Moot point now I spose.
I run my bike with a permanently blocked filter bypass as of 9 months ago. The bypass cavity had severe damage where the spring seated. Useless.
I change oil and filter at 5,000 k's. No issues thus far.