you have a couple of options....
but before i have a couple of suggestions whether you choose the options below, or not to at all. First all...when trying to root clones...72-78F is optimal. Once roots pop....drop temps no higher than 68F. Keeping your res cooled and chilled is VITAL to explosive root growth.
Also, I've been drilling since day one. DONT BE AFRAID OF ROOT STIMULATORS. They are your friend, trust me. Roots Excellator or Rhizotonic.
Option 1:
Use a deburring tool and/or a dremel type device and widen up those holes on the ezcloner. Then put in your netpots. Word of advice, and i know you arent a dummy. BUT most netpot without lips normally it is a good idea to use a 1 7/8" holesaw instead of 2" because you always wanna take off 1/8" when drilling so just incase you dont have a lip on your netpot you will have support. However me and you use the same netpots. and yes i can tell.
they have good lips...however on my cloner i built, i still drilled 1 7/8" holes.
option 2:
stick with just using neoprenes in the ezcloner and charge the ezcloner nute soup with a root stimulator aka roots excellator or rhizotonic and hit them with a heavy dose. give some transition nutes let them veg and boom put them in the aero. Keep in mind, do this as soon as all have popped roots. No nutes before roots imo (unless its a rooting/cloning solution and/or some rooting stimulators)
option 3:
stop acting like a little bitch. you and I are both the same, i know we strive for perfection. but you wanna know a secret? you know that aero cloner i built? yea yea i cracked the last 2" hole too...BFD? yea big.fucking.deal!!! pressed the fuckit button and kept on moving. i used some gorilla glue (waterproof & paintable) and you cant even tell unless i point it out to you or you are physically looking at it real time, tangible shit. i coulda smoothed it out, but fuck it...the black and white paint still has my cloner looking sick as fuck. matter fact i just took it back out of storage and washed it down... the damn thing still looking brand new as fuck.
you suffering from end game doubt man. you almost there.... dont let that shit get you down. if you really are anal...just get another top. i got 3 tops. you know how it goes. we get picky.