Get one of these - it makes regraining a breeze.

http://solutions.3m.com/wps/portal/3M/en_US/3MIndustrial/Abrasives/Products/~/Scotch-Brite-Combi-R-Wheel?N=7581713+3293241140&rt=rud

While doing a top to bottom restore on your JO will involve some different skill sets, it won't come close to the challenges you are experiencing here. Playfield restoration will be your biggest challenge. If you can get through prepping your AFM cabinet you will find EM cabinet restoration a welcome challenge. You get a lot more immediate satisfaction as you go.

In the end it's all relative. I did a playfield swap of a High Speed late last year and swore at it for a long time, mostly because I didn't have the right stapler, and man does HS have a crap load of staples. Right now I'm doing a Monster Bash playfield swap and I like it a lot more just because there aren't all the staples. It probably is similar in the overall work needed but I'm more at ease with it.

As for your JO restore, if you want to make your needs from the EM community easier (on you and on us), get the game playing solid 100% before you tear into it. The last thing you want is to chase problems that you don't know where they came from.

As long as your intent is to address those deficiencies in playability BEFORE you tear into it then you should be fine. Frankly it is recommended that you get them fixed and play it for a while to gain insight into the game itself and a deeper benchmark to refer to.

As for working through the issues, we are here.

The stepper is probably gummed up mech or broken wire.
The score reel is what it is, they get sluggish and can usually be addressed without a full teardown.
Targets not resetting is probably a switch, broken wire, or blown fuse(s).

To add to the JO plan, and since they are modular, it is not unreasonable to totally refurbish the main relay board and head relay board and get the game fully playable before you approach anything cosmetic.