You can use HRV...
Heart Rate Variability is the variation in the time interval b/w heartbeats. By measuring this along with your heart rate you can measure your ANS (Autonomic Nervous System) = the resulting data allows you to decipher your body's stress & recovery processes.
All you need is a heart rate monitor + smartphone app + 3mins in the morning.
This data along with how you feel = you'll be able to make a more informed decision on your training/recovery.

If you stop making progress,,feel tired,,start noticing strains pains and injuries,,,then chances are you are overtraining.

Rule of thumb keep up a high intensity workout to just under 1 hour. Eat like you want to succeed. Rest like you want to succeed. If you need more then switch up to a split routine and go 2x a day.
Rest
Eat
Work.

How many sets/exercises for each body part do you do? Something to try might be a system similar to how Dorian Yates (surprise) trained back in the day, or what is now called HIT training. It's a style of training influenced by Mike Mentzer and Arthur Jones of Nautilus. It's basic ethos is that volume and intensity are key...train heavy, to failure or beyond using forced reps, negatives, etc, using minimal sets.

Perform 2 warmup sets on the first exercise for each muscle group (let's say starting with incline chest press) the second being heavier than the first. First set do about 15 reps, the second 10-12, neither to failure. The third set is the final and only working set, done with heavy enough weight so that you reach complete failure by 6-8 reps. For the next exercise of the same body part (let's say flat bench) you do only one warm up set, then another single working set very heavy... to failure again by 6-8 reps. From here, you may do a warmup or perform only the one working for the next exercise (perhaps Pec Deck Or Dumbell Flys). Finish chest with something like a single working set of Cable Crossovers to failure. The idea is that since muscle fibers are already fired up, there is no need for any more warm ups. Workout days are an hour max, typically more like 45 minutes.

There are lots of videos on YouTube and even a little training program on bodybuilding.com of this, with him and Kris Gethin performing it full body all the way through.

Here's a link to an article where he explains it a little bit more in depth as well: http://www.musculardevelopment.com/training/2852-principles-of-mass-cons...

I used to kill it at the gym for 1 1/2 to 2 hours, 6 days a week. Since then, I've cut back to 1 hour with no other change, & I've noticed a huge improvement. I've been off cycle for 9 months now, & I'm not sure if I'll stick with 1 hour or step it back up when I start my next cycle.

I'm only in the gym for 45 minutes,my workouts are very intense,some people I know workout for two hours a session,I've had a few people train with me and they never turn up again they would rather talk and piss about in the gym so I don't waste my time with them.You can definitely overtrain I have done it in the past and you know when you have.

Think about people that do manual intensive jobs all day such as shoveling for 12 hours, and you think doing an hour in the gym will give you over training please. for example their is a marathon runner that did 7 marathons in 7 days and his body just got stronger and fitter. So i doubt to much about over training. Your body adapts to its surroundings and pressures.

If the muscle your training isn't pumped, fatigued, or burning under 1 hr. Your not pushing yourself hard enough. Your Doing It Wrong! No such thing as overtraining only under nutritioned or not enough sleep.

You dont need to spend hours in the gym for results. Scientific proof shows that after 30 minutes to an hour your muscles are beat and the lactic acid is building up hindering growth. Muscles grow when you rest and feed them. In the gym you are tearing them relentlessly and they do not immediately go into repair mode. I do about 20-30 minutes in the gym but I only do 3-4 sets at around 3-10 reps but I go 85-95% 1RM. Since swapping over to this about a month ago my bench went up 100 pounds and so did every other exercise I do. Less reps more weight for strength you leave the gym in about 30 minutes. More reps less weight you should be out the door in 60. Any more then that you better be on the treadmill.

When it feels like you have been hit by a bus then take a few days off.

Overtraining signs for me are 1) noticeable sex drive decrease 2) extreme difficulty falling asleep

Are you getting any respect?
Congratulations on your weight loss by the way I hope you are healthy and feeling better.
Stick to that nutrition as hard or even harder than training. Maybe take out arm day since you work chest and tris then back and bis then shoulders to get an extra rest day, strict cardio day or abs.
If you feel tired or muscles exhausted just rest and try again the next day or enjoy the weekend and then get back. Listen to your body if you feel good great if you're tired rest.

Blood work. Dropping 90lbs in a few months isn't healthy.