Need clarifying on Experience Factor

The HUBs text doesn't mention splitting it, it just lumps all EF gain together.

Experience factors (EFs) are gained by totaling an adventure
party’s experience factors of foes defeated, killed or captured;
10% of every silver piece of market value of relics and treasure
taken through adventuresome exploits (as opposed to commerce,
trading water, etc.); plus GM issued rewards of factors
for individual bravery, clever use of skills and relics, mutations
and implants in creative ways, etc A GM can hand out EFs in
d20 or d100 units at any time to an individual character if he
or she thinks the character deserving.

Personally speaking, giving them all the total EFs makes them progress really quick when they went through the Mall of Doom they went from level 2 to 9 after finding a grenade and room filled with sleeping moaners, and so I had a bunch of extra work adapting the difficulty to keep it fun.

Options to slow down EF gain. 

• Splitting the total earned EFs between the party, everyone levels up at the same time.
• Point buy, after each level up PC's total EF reset to 0 on after each level up.
• Players only earn EFs from enemies they've hit, this is more work and can mean strong fighters progress faster than non-combat characters, though this can be offset with d10/d20/d100 EF rolls for using skills like medic, lock picking and the like. 

You'll probably find quickly like I did that leveling up is a pretty big advancement in TME. That's not a bad thing... this game is way deadlier than most RPG's. Don't be afraid to let them advance quickly; there's more than enough in the wasteland to challenge even the highest level character.

Besides, the more powerful they are the quicker you can throw the REALLY monstrous stuff at them!

Tim

According to the rules EF gain should be done at the end of the day when the characters rest (but obviously what works for your group matters more) but that should work nicely, might be worth making it so only silver EF they earn is what they manage to sell, since they'll no doubt keep some of the fancy stuff for themselves anyway.

Same. EF is something I've been looking to modify in my own games.

What's tripping you up on the skills, is it just when?

I do skills increases when we do the level up at sessions end, my players had real trouble with the idea that they couldn't just increase any skill they wanted.

+d4 for skill points to spread around, or all to one skill?
The hub rules doesn't say you need to spend it on one skill. So you can spread it around or dump them all on one skill.
-Though I personally I've implements an staggered cost if they want more than one point in a skill per level*

And it only goes to skills used or the newly acquired?
Has to be used on a skill used on that level up. Though not all skills can be gained through a level up alone.

Possible new skills
if used, even unsuccessfully 
Climbing - Dodge - Gambler - Grapple - Riding - Stealth
- Tracking - Brawling (see Unarmed Combat) - Weapons Expert


Skills that need an existing point before level up.
Disguise Artist
- Driver
- Erotic Arts
- Forgery
- Gun Slinger
- Gunsmith
- Junk Crafter
- Knife Fighter
- Knife Thrower
- Lying
- Medic
- Navigate by Stars
- Negotiating
- Pick Locks
- Pick Pocket
- Pilot
- Relic Knowledge
- Sniper
- Tech, Bio
- Tech, Chemical
- Tech, Computer
- Tech, Electrical
- Tech, Mechanical
-Tech, Robotics - Tracking
- Martial artist (see Unarmed Combat)
- Wilderness - Survival


*One player got a single hit with a gun then got 8 skill points and put them all in weapon expert: Shotgun, this meant their Shotgun attack was base SV +50, Shotgun+ 20 +WE+ 20 So basically they could only miss if they rolled 1-10. So as an example if one of my players wants +3 in one skill in a single level up they'll need to spend 6 points. Though I do award skill points for amazing plays, super lucky shots, and the like.