OMG Jo!! I'm sooooo sorry!!

We just got back from being at my parents house after church.
Sounds bad.

Poor little guy! He's really having a rough time.

Sounds as he does in fact have a tummy bug.
Since wi/wo isn't established and you have the ability (no other lo to care for) I would go back to your primary way of putting him down (patting). I never think its right to do new sleep training with any illness going on. In other words I don't 'change up the game' when they are ill. Its not really fair to him as that is the only way he knows how to go down when not well. You can always get a fresh start after he is well.
When on the set nap/bt and the nap was a 'no go', we just did bt when she could no longer tolerate being awake. So we did a couple 5pm bt's. Its okay to do that here and there until you get that nap well established, especially if they are teething and just can't make it. I don't do it ever on a regular basis as it will set their body clocks to that time... the older they get the easier it is (with constant early bt's) to set their clocks to that time if always put down then. Then you get in the early bt/ early waking cycle.

So I stretch until I know we just need to put her down, and then I do it. I also find as they get older they don't fight nap/bt b/c of OT, they crash out.... baby and toddler sleep are quite different. As they get older things change.
Sounds like your extra communication is working for bt. I would keep that up FOR SURE! Really prepare him mentally and give him time to get himself ready to go down. Spirited kids need more time sometimes than others. Trying to portray it as a good thing sounds like its working too (we need to let our bodies rest so we can get up and play more, everyone has to rest so we feel better and can have more fun exc..........)
KATIE YOU ARE SOOOOOOO RIGHT!! If you or DH can stay in the back seat with him on the way home from church to give him snacks/ play with him to keep him up that's best. Then do wind down and nap time.... other wise he's at the age he'll start to sometimes refuse the transfer.
Sounds like you might need to just stick with the patting and ride it out until he's well. Later then you can asses it with DH and decide if you want him to learn to go to sleep another way. But I wouldn't forge ahead at all with him being ill. Just love and comfort for now.
Sure hope he gets better soon!