Rough/pulsing engine & Check Hybrid System

I've been working on this for about 6 months and out of ideas.
I have a 2010 Prius with around 170,000 miles. Near the end of 2025, the engine started running rough with a pulsing/surging sound and threw a check engine light. I had it scanned at O’Reilly and was told it was related to the EGR system, but I no longer have the exact codes (I can try to track them down if that’s important).

Over the next few weeks, I removed and cleaned the EGR valve and cooler, cleaned the intake manifold (there was oil pooled inside), and replaced the PCV valve. After putting everything back together, the car ran a bit better but still didn’t sound quite right. The check engine light did not come back at that time.

In January, I took it on about a 2 hour highway drive. By the end of the trip, the engine started making a pulsing/surging sound again. After letting the car sit for a couple of hours, I started it again and it ran extremely rough right when the engine kicked on. I got the red triangle warning and a "Check Hybrid System" warning, and the car basically died and would not accelerated. I shut it off, restarted it, and was able to limp it to a safe place to park and eventually get it towed home.

I took it to a local mechanic (not a Toyota dealer). After diagnosing it, he said the hybrid battery needed to be replaced and believed that would fix the rough running and may have actually been the original cause that threw the EGR related codes as the battery was likely failing at that time. He also inspected the cylinders with a camera and said he didn’t see signs of a head gasket issue.

Since a new OEM battery was quoted to my by my local Toyota dealer at ~$5,500, I decided to try recondition the battery myself. I cycled all the modules multiple times through discharge/charge cycles (up to about 20 cycles) with the goal of getting >5 aH consistently per module. From what I found, “healthy” modules should be >5 aH, but most of mine wouldn’t reach that. I aimed for at least ~4.5 aH per module because replacement modules on eBay weren't advertised to be any better, then balanced the pack and reassembled it based on each modules best performance (all data below).

After reinstalling the battery, the car seemed to run better at first on a 5 mile drive but I could still hear a pulsing/surging engine. The next day, within a 10th of a mile, I again got the “Check Hybrid System” warning along with a check engine light. I don’t have an OBD2 scanner and it’s difficult to get the car somewhere for another scan.

I’m trying to figure out whether this really is still a hybrid battery issue or if something else is causing the rough/pulsing engine. Does this sound like a battery problem, or should I be looking at something else, or even a head gasket despite what the mechanic said? Did I recondition the battery incorrectly or incompletely? Did I rebuild the battery packs incorrectly?

Bottomline, what should be my next step?

Below is a csv of all my data from the battery reconditioning as well as how I rebuilt the pack.

Code:

Module,Pre-reconditioning Voltage (oc),Discharge 1,Charge 1,Discharge 2,Charge 2,Discharge 3,Charge 3,Discharge 4,Charge 4,Discharge 5,Charge 5,Discharge 6,Charge 6,Discharge 7,Charge 7,Discharge 8,Charge 8,Discharge 9,Charge 9,Discharge 10,Charge 10,Discharge 11,Charge 11,Discharge 12,Charge 12,Discharge 13,Charge 13,Discharge 14,Charge 14,Discharge 15,Charge 15,Discharge 16,Charge 16,Discharge 17,Charge 17,Discharge 18,Charge 18,Discharge 19,Charge 19,Discharge 20,Charge 20
1,7.95,3295,5042,3286,6500,3572,6500,4334,6500,4260,6500,4505,7000,4766,7000,4742,6500,4885,6500,3932,6500,4841,6500,4911,6500,5191,6500,4894,6501,5112,6500,4884,6172,4780,6500,5033,6500,5090,6500,,
2,7.96,3547,6500,3826,6500,4048,6500,4152,6500,4090,6500,4547,6500,3495,4982,4140,6500,4599,6501,2595,6501,4460,6500,4514,6500,4742,6500,4580,6500,4533,6500,4606,5450,4391,6500,4488,6500,4836,6500,4686,6500
3,7.95,1422,5578,2671,6440,3139,6478,3565,5611,3775,5926,3841,6500,3308,7000,4516,7000,3453,6500,4896,6500,4520,6500,4981,6500,5012,6500,4636,6500,5081,6501,4873,6500,4765,6500,4791,6500,4958,6500,4882,6501
4,7.97,1933,6010,2935,6500,3396,6500,3629,6500,3497,6500,3898,6500,3386,7000,4471,7000,4481,7000,4442,7000,4437,7000,4234,7000,4905,7000,4736,6500,4925,6500,5069,6500,4146,6500,2444,6500,4913,6501,4980,5396
5,7.95,1821,4360,2844,4460,3101,6500,3960,6096,4181,6500,4233,6500,3743,7000,4568,7000,3836,6166,4790,6500,4708,4544,4017,6501,4741,6500,4773,6501,5027,6500,4896,6500,5125,6500,,,4874,6500,4812,6500
6,7.94,1222,5614,2645,6500,3188,5708,3373,5355,3540,6500,3816,6500,3396,7000,3923,7000,3792,7000,4213,7000,4556,7000,3834,6501,5092,3606,3175,6501,4894,6500,4830,5745,4660,6500,5222,6500,4867,6500,5113,6501
7,7.94,1411,5220,2772,6248,3312,4950,3466,5487,3796,6500,3866,6500,4690,6500,4793,6500,4878,6500,4745,5588,4597,6500,4971,6500,4643,6500,4771,6501,4867,6501,1748,6500,4896,6500,5125,6500,4874,6500,4812,6500
8,7.94,2379,5139,2748,5551,2904,5457,3060,5711,3208,5734,3228,5968,3222,6089,3541,6152,3651,6423,4258,6310,3212,7000,4437,7000,4457,7000,3945,6500,4639,6500,4774,5961,4858,6500,4894,6501,4919,6501,5127,6500
9,7.97,2374,5653,3277,5816,3632,6370,3993,6500,3935,6500,4295,6500,3531,7000,4369,7000,4603,7000,4070,6501,4924,6500,4881,6500,4763,6501,4782,6500,4966,6500,4908,6500,4911,6500,4989,6500,4993,6500,4763,6501
10,7.96,3201,6500,4219,6500,4156,6500,4186,6500,4692,6500,4349,6500,3698,7000,4745,7000,4621,7000,4841,6500,4825,6500,4535,6500,4633,6500,4708,6500,4908,6501,4710,6500,4907,6500,4732,6500,4693,6500,4905,6501
11,7.94,1547,4794,2370,5183,2809,5508,3155,6107,3475,6215,3695,6500,3231,6500,4164,6500,4313,7000,4191,7000,4423,7000,4441,7000,4681,6500,3934,6214,4926,6500,4709,6500,5058,6501,4872,6500,4739,6500,4738,6500
12,7.94,1278,4541,2589,5550,3170,6090,3545,6500,3570,6500,3874,6500,3288,6500,4136,7000,4110,7000,4266,7000,4235,7000,4258,7000,4665,7000,4896,6500,5013,6500,4311,6398,4979,6500,5134,6500,5128,6500,,
13,7.95,1331,5074,2766,6217,3376,6500,3912,6500,3946,6500,3966,6500,3828,6930,4848,7000,4833,7000,3674,6500,4680,6501,4646,6500,4898,6501,4719,6500,4688,6501,4812,6500,4687,6500,4737,6501,4822,6500,4759,6501
14,7.98,3168,6500,4298,6500,4332,6500,4436,6500,4611,6500,4631,6500,3521,6500,4762,6501,4612,6500,4905,6500,4669,6500,4603,6501,4901,6500,4940,6500,4645,6500,4630,6501,4450,6500,4486,6500,5034,5512,4484,6500
15,7.94,2474,6083,3405,6500,3843,6500,4954,6500,4986,6500,5545,7000,3890,6500,5021,6313,5123,6500,,,,,,,,,,,,,,,,,,,,,,
16,7.94,2246,4482,2986,5482,3482,6196,3964,6500,4486,6500,4250,6500,3595,7000,4792,7000,4123,6500,4864,5979,4917,6026,4734,6500,4892,6500,5117,6501,5019,6500,,,,,,,,,,
17,7.97,3384,6500,4495,6500,4456,6500,4489,6500,4449,6500,4817,6500,3827,6500,4676,6500,4796,6501,5091,6501,4872,5929,4839,6500,4778,6501,4785,6500,5063,6500,5122,6500,,,,,,,,
18,7.95,1292,4464,2526,5512,2866,5868,3279,5318,3510,6370,3601,6500,3128,6383,4144,6199,4270,6433,4277,6500,4576,7000,3535,6396,4857,6500,5036,5916,4776,6500,4890,6501,5157,6500,5194,6500,,,,
19,7.96,1868,5829,3190,6500,3640,5467,3884,5881,4058,6081,4143,6500,3077,7000,4102,7000,4140,6894,4502,7000,4626,7000,4536,6500,4525,6500,4630,6500,4431,6500,4556,6500,4709,6500,5007,6500,4711,6276,4932,6500
20,7.94,1242,5666,2920,4839,3301,4844,3507,6500,3597,6500,3882,6500,3383,6500,4263,6485,4299,6901,4141,7000,4281,7000,4299,7000,5199,7000,4148,5897,5037,6256,4976,6500,5008,6501,5182,6501,,,,
21,7.97,2024,4560,3178,4842,3493,6500,3968,6500,4281,6500,4312,6500,3617,7000,4622,7000,3591,6501,4686,6500,5076,6495,5038,6500,,,,,,,,,,,,,,,,
22,7.94,2109,5510,2742,5698,3185,6413,3692,6500,4019,6175,3953,6500,4031,6500,4627,7000,4533,7000,4624,7500,3999,5789,4810,6501,5146,5028,4328,6500,5217,6500,4918,6500,4959,6500,5092,6500,4924,5905,4945,6501
23,7.96,2434,5936,2970,6500,3257,6500,3251,6342,3720,6500,3900,6500,3133,7000,4392,7000,4365,7000,4701,7000,3669,4959,4175,6500,4855,6501,4837,6501,4689,6500,4870,6501,4986,6500,4986,6500,4888,6205,4901,6500
24,7.97,2272,4655,3131,5334,3470,5818,3759,6442,3740,6500,4159,6500,3538,7000,4175,7000,4616,7000,3716,6501,4869,6500,4551,6278,4814,6501,4965,6501,4594,6500,5012,6500,4831,6500,4690,6500,4700,6500,4853,6500
25,7.96,2204,6500,3031,5407,3587,5525,3826,6500,3991,6500,4273,6500,3623,7000,4746,7000,3903,4860,4108,6500,4843,6500,4958,6500,4776,6500,4988,6500,4761,6500,5086,6500,5239,6500,,,,,,
26,7.97,1653,4021,2628,6331,3177,6256,3599,6500,3809,6500,3922,6500,3341,7000,4207,7000,4770,7000,3695,6500,4872,6500,4817,6500,4743,6500,5020,6500,4882,6500,4830,6500,4658,6501,4789,6500,4744,6500,4724,6500
27,7.96,3741,6500,4247,6500,4352,6500,4486,6500,4490,6500,4541,6500,3599,6500,4635,6500,4589,6500,4626,6501,4711,6500,4620,6500,4590,6500,4782,6500,4609,6501,4896,6500,4576,6500,4925,6500,4925,6501,4601,6500
28,7.94,2326,5182,3369,6500,3869,6500,4065,6500,4171,6500,4385,6500,3991,7000,4326,7000,4549,7000,3649,6500,4311,6500,4365,6500,4931,6500,4573,6500,4758,6500,4652,6500,4583,6501,4809,6500,4690,6500,4678,6500

Below is how I rebuilt the battery packs:

Code:

Pack,Module,Max mAh
1,15,5545
1,25,5239
2,6,5222
2,22,5217
3,20,5199
3,18,5194
4,1,5191
4,12,5134
5,8,5127
5,5,5125
6,7,5125
6,17,5122
7,16,5117
7,3,5081
8,21,5076
8,4,5069
9,11,5058
9,14,5034
10,26,5020
10,24,5012
11,19,5007
11,9,4993
12,23,4986
12,28,4931
13,27,4925
13,10,4908
14,13,4898
14,2,4836

I know this is long and a lot, so thanks so much for reading this, and thank you if you're able to provide some help!!