I am a songwriter and composer - in the sense that I write lyrics and also compose the guitar music to go with the lyrics. And the only notation I feel a need to write down is the chords I am playing. So we have a few things in common.
When I write my lead sheet, I have the lyrics typed out and then I use a pencil to put the chords in the exact place where the first strum of that chord will occur. This helps with the rhythm when I am playing the song. If the chord is strummed between two words (notes in the melody) - I write the chord name between the two words to so indicate.
After I write the lead sheets with lyrics and chords, I record my songs. But after that - I have personally never felt a need to transcribe my music into notation. But I can see where it would be a great learning tool to further your music education if that is of interest to you.
So if I was going to transcribe my music and I knew the notes (as you say you do) in order to get the rhythm part down (that's what you said you had the most trouble with) here is what I would do.
First - I would record the song to a drum track in whatever tempo I wanted to use. Or perhaps for purposes of transcribing the rhythm, I might slow the tempo of the drum track way down. Some recorders will allow you to do a slow speed playback of your final recording.
I use a multi track recorder with built in drum tracks. There are several made by Boss, Tascam and Zoom to name some of the most popular. Here is one by Zoom that has hundreds of built in drum loops that you can set to whatever tempo you want Zoom 8 Track Recorder
When using one of these with drum loops, the first thing I do is find a drum loop that best replicates the rhythm of my song. Then I choose a tempo and record the guitar chords while playing over the drum track to keep a consistent tempo. I select a drum track with a strong accent beat that allows me to hear when each new measure starts. After I track the guitar chords, I go back and sing the lyrics, thereby establishing the melody. Of course you could use an instrument to play the melody instead of singing it.
If I now want to transcribe what I recorded, I have narrowed down how many notes are in each measure by listening to the drum track. I can also hear how the drum beats fall in relation to the notes I sing, so I will know which beat the note hits on. I can rewind and play each measure over and over until I have the rhythm notated for that measure and then move to the next.
Another way to do this if you don't have or want to spend between $200 - $300 U.S. for a multi-track recorder = would be to use a digital metronome like this one Boss DB-30 $39.00 U.S.. It doesn't just go tick tock like the manual metronomes. It has nine rhythm types and 24 beat variations and can tick the eighth notes or quarter notes etc. while tocking (accent beat) the beat you tell it to (beat 2 and 4 - beat 1 and 3 - just beat 4 - or in 3/4 time - just beat 3 etc.).
And using a 1/8" TRS to 1/8" TRS cable you can plug this into your i-phone, or computer microphone in jack or use a hand held digital recorder like this Sony digital recorder $49.99 U.S. which has a mic in jack that you can plug the metronome into and record the drum track directly into the recorder which will interface with your computer via USB.
So you select and record a click track that matches the rhythm of your song, then record yourself playing guitar to the click track. All of the recorder options mentioned (including your phone) have external microphones that you can use to record your guitar or singing. Or you can get an interface for your smart phone like this one IK i-rig for guitar - and plug your guitar directly into your phone and play it while listening to the previously recorded click track now saved on your computer (use headphones to listen). You can connect the recorder or your phone to your computer and download each track into free audio software such as audacity.
After you record the guitar part over the click track, when you play it back, you will clearly hear the rhythm. You can also then record the melody by singing or playing it and add that to your recording so you can hear which beat each melody note is played or sung on and how meany beats it is held and and if there are any pauses (rests) and so on.
This process should help you get a "feel" for notating the rhythm by listening to the rhythm on a drum track or customized click track - along with the melody.
I certainly think that would make the process easier for you so you might be more inclined to start transcribing your music. Who knows, as you master the skill of music notation - you might find it almost enjoyable as composing the music to begin with.
Good luck with your musical journey. Mostly keep it fun!