fellow trainerroaders

I don't follow trainerroad's plan to the letter (ex: they call for Tues/Thurs/Sat, but I do Mon/Wed/Sat). It's possible that a really hard run is impacting your ability to perform the next day, but it's also possible that it was just a bad day (they happen). Maybe it was a bad day on the bike, or maybe you went a little too hard on your hard run - especially if you just started hard runs. It's something you need to ease into so going too hard to early can definitely cause problems. I wouldn't make any decisions based on one bad session. The only alternative is to schedule your hard run on Sunday to give yourself an extra day recovery before your next ride.

A jump in FTP from 236 to 272 in 3 months is huge!

Are you getting enough to eat before the run workout? One of the TR podcasts talks about it being difficult to do VO2max workouts in the morning due to not having sufficient fuel. I assume you don't eat in the morning before your workout, but did you eat enough the night before?

What you are describing happened to me four weeks ago.

I'm also following the Trainerroad mid volume Olympic plan. I'm currently in week five of the specialty phase. Like you I saw an FTP increase (40 watts) when I re-tested at the beginning of the specialty phase. The workouts were noticeably harder after re-assessing FTP (which is expected). I managed to complete week 1 and the first two workouts of week 2. However I hit a wall during the longer weekend ride of week 2. I was pretty discouraged.. I made some adjustments to my swim and run training though and I've managed to hit all my workouts since then. Here's what I did and maybe you can get some ideas to apply to your training.

warning/disclaimer: I'm not a coach or even a very good athlete. This is just anecdotal for your consideration.
1. I incorporated more rest and recovery at the expense of swim and run sessions.

I don't follow the Trainerroad swim/run suggested workouts. I still feel really guilty/concerned about this, particularly with the run. I'm a big proponent of more run mileage by way of high frequency. So it kills me to cut my mileage. I was logging 30 miles a week on 5 runs. Now I'm running 21 miles a week on 4 runs. I was swimming three days a week and now I only swim two. Swim is by far my strongest event. This is temporary as I don't feel good about only two swim sessions a week over the long haul.

2. I ditched an extra ride.

I did Mid Volume Oly for the build and specialty. During base I followed the high volume. At the end of the base I took a look at the rest of the high volume plan and determined it was too much for me, but I thought I could handle more than what the mid volume suggested. So I added in another long aerobic ride on the weekend. I kept this through the build and week one of specialty, but it just became too much for what I'm capable of.

Prior to these changes my training hours were in the 11-13 hours per week range with no planned days off (emphasis on planned) and early morning workouts every day. Now I have a planned rest and recovery day PLUS two additional days where I am only working out 1 time that day and the workout is not a morning session (which means more sleep).

I still do a hard run on Wednesdays (nestled in between rides 1 and 2 from TR on Tues and Thur), but all three of these workouts happen at the same time in the AM. I seem to be able to handle this. I do my longest run (9 miles) on Friday morning, Saturday is an off day, and Sunday morning I do the longer Trainerroad ride. The first run of the week as suggested by TR seems like it is just there to accumulate miles. You could try splitting that into two shorter runs on different days if you think that would help. This is my third week doing this and it seems to be working for me.

Last but certainly not least, I'm noticing the rides are easier but that should not come as a surprise as my fitness should be improving as will yours.

I race in three weeks. We'll see how it goes that day. Based on how that race turns out I'll make adjustments to my schedule. I'm eyeballing another race in mid July and if things go well for the upcoming event I may just repeat what I did for this one. I'm really happy with my gains on trainer road though. It is just a matter of finding that balance where I can run as much as possible without inhibiting my ability to hit my bike workouts. That is my main objective.