What's your wattage?

[TxDoc]

One problem I have with estimating my FTP other than the boredom factor for doing a 1 hr effort on the CT is that in general, my 20km TT is much better compared to my 40km TT. This is going by how I place relative to others, particularly in Merckx-style TTs. So, what does that mean for my FTP? That it really is pretty low but I probably follow more of a pursuiter power profile? (I haven't tested it, but I'd guess that to be the case).

Yes and No...
If your average power for 20' TT or 30' TT is much higher than your avg power or normalized power for 60' TT, the main thing this tells you is that your muscles fatigue much more after 30', which makes it hard for you to sustain a high power output when the effort lasts longer.

The 'profile' you refer to when you speak of 'pursuiters' (high sprint max, and big drop moving towards threshold) is the so-called power profile.
What the power profile tells you is where your power/weight is in each area. In fact usually it takes 5'', 1', 5', 20'. So the power profile by definition looks at sprinting power (5''), anaerobic (1'), VO2max (5'), and FTP (20'). What it does is paint a picture of what your cycling abilites are in the various zones. When you look at the power profile - yes, you may differentiate sprinters from time trialists, pursuiters, etc.

What you are actually doing, by comparing 20' and 60' - is to compare different tests in the same zone, which in this specific case is the lactate threshold area. So in fact, when you do that, you are looking at what most people call the fatigue profile and not at the power profile. The fatigue profile looks at one zone, and determines what is the status of your fatigue resistance.
For each zone there are some set percentages that coaches use to define fatigue resistance below, above, or at average. So you could make one fatigue profile for the VO2max zone, one for the threshold zone, etc...

In simple words - the power profile compares different zones, while the fatigue profile is specific to one zone.

So in your case, if you want to look at the lactate threshold zone - take your average power from your 20' TT, from 60' TT, and from 90'TT. If you do not have TT data for 60' and 90' you can use normalized power at 60 and 90 from a hard ride, although it will not be as accurate (but very very close!).
In average, we usually expect that the 60' value will fall between 4% and 6% lower than your 20' value. Likewise, the expected average for the 90' value is about 8-14% lower than your 20' value.
If you notice a larger drop when you compare 20' and 60' (i.e. your 60' value is less than 94% of your 20' value), what this tells you is that your fatigue resistance at threshold is below average.

Not sure this is written in a way that sounds reasonable, I'm post-call and kind of tired tonight so I may speak some nonsense...
If you would like some tables or info to calculate your profiles send me a PM, I can probably send you some.

And again if you want to test your fatigue profiles, CT is fine for threshold and maybe VO2max depending what you work on - but less accurate when you talk max, so the neuromuscular and anaerobic levels are harder to test well on CT.

So, when doing FTP-based CT workouts (erg files programmed to put you at x % of FTP for each interval), should I continue to set my FTP on the high side considering that those workouts are relatively short?

If most of the intervals in your workouts are within the 20 minutes duration or so, yes you could as well use the FTP value that you calculate either from a 30' TT or from a standard 95% of your 20'TT average power. For short interval workouts the % error would not be that much.

One day, an SRM will be in the budget. One day.

I guess this is where the CycleOps people did it right - the PT sits in between, with practically the same amount of data and accuracy of a quarq/SRM and a price which is not that much higher than a CT. And it allows cheap options - I'm one of those people who went cheap to begin with, and I still use a wired PT now that everyone has wireless computers... The benefits of collecting the data completely outweigh the hassle of seeing a wire on the bike and having to change wheels.

Good luck y'all, I'm going to sleep...