The bottom edge of the logic board has a rubber sponge that pushes the logic board up toward the clickwheel and display. It may help to reach in with a spudger and push the logic board downward, compressing the sponge and giving one a tiny bit more clearance between the logic board and the clickwheel.

Agreed that the iFixit battery does not fit. The current (2022) battery is significantly taller. Like you said, if also replacing the hard drive with a compact flash, your method of removing the hard drive rubber bumper gives you some more room for the taller iFixit battery. And like you say, the rubber bumper really isn't needed with a compact flash as it's a shock absorber of primary use with a hard drive.

Reassembly notes 3 (supplement to recommended procedure):

I used 4mm double stick tape to secure the bezels (I didn't scrape off the existing adhesive as it was mostly gone anyway). I put the tape on the circuit board end connection points not the bezels themselves.

Before installing the end bezel with the lock switch, check that it is still in the locked position. This needs to match up with the position of the switch on the logic board.

Reassembly notes 2 (supplement to recommended procedure):

When the circuit board reaches the point where the battery wires are at the housing opening, you will probably need to tuck them in with a spudger to avoid getting stuck at that point.

For the very last part of inserting the logic board, there's no choice I found except to push on the headphone board. This is not ideal. Push on the end nearest the connection point of the headphone logic board to the main circuit board.

Check operation before installing the end caps. Slide the "lock" switch with your fingernail to the "on" position during this testing. Once satisfied with your testing, turn off the iPod and slide the lock switch back to the "locked" position.

Installing the circlip metal bracket is best done with snap ring pliers.

Reassembly notes 1 (supplement to recommended procedure):

When starting to insert the logic board into the housing, note the channel in the housing. The circuit board inserts on the side of the channel facing the rear of the housing (not on the side facing the display).

Grasp the circuit board from the side as much as possible. Note that the end of the circuit board has the headphone board attached, and it is just secured with a very small jack. It cannot take much force of pushing the circuit board into the housing. It's very difficult to find a spot on the end of the circuit board itself as a pushing point, even with a spudger.

Upon reaching the click wheel board, the circuit board may catch. There is a flexible sponge located on the leading edge of the circuit board that presses toward the display side of the housing. Reach in from the bottom of the housing with a spudger, and press downward slightly (away from the display side of the housing), while gently pushing the circuit board into the housing.

Don't grab and pull from that top piece as it's the headphone logic board which is only connected to the main logic board with a small molex connector.

Note that the current battery sold by iFixit will not fit. The battery connections protrude on the top and interfere with the headphone board and the battery connector. Find another vendor for the battery.

The battery is stuck to the logic board with a small square adhesive pad (seen in the next picture). It may adhere to the battery as shown, the logic board, or may tear and split as you remove the battery. Transfer as much as possible to the new battery, perhaps securing with a piece of double-sided tape.

Note the polarity of the wires so that you don't attempt to plug in the new battery the wrong way.

The molex connector has raised edges on each end that one can catch with a fingernail. Do hold down the mating connector on the logic board with a spudger to avoid stress.

If you push as pictured with your thumb, you may end up pushing on the clickwheel board. Press more from the lower edge, small finger with fingernail pointed opposite from the picture, away from the clickwheel/display side.

To avoid losing the screws, if you have any kind of magnet such as a refrigerator magnet, place the screws on it for temporary storage on your work surface.